From sbrozell at scripps.edu  Tue Oct  2 17:04:26 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Tue, 2 Oct 2007 17:04:26 -0700
Subject: [Dock-fans] Fwd: Re:  Fwd: Re:  Parallel install
In-Reply-To: <509560.5241.qm@web57612.mail.re1.yahoo.com>
References: <509560.5241.qm@web57612.mail.re1.yahoo.com>
Message-ID: <Pine.SGI.4.51.0710021703220.26335@pusar.scripps.edu>

Hi,

On Fri, 28 Sep 2007, Francesco Pietra wrote:

> Commenting out the two last lines on my .bashrc
>
> #For amber9
> MPI_HOME=/usr/local
> export MPI_HOME
> AMBERHOME=/usr/local/amber9
> PATH=$PATH:$AMBERHOME/exe; export AMBERHOME PATH
>
> the issue was fixed:
>
> install/test/amber_score_181l
> shows
> Running: $DOCK_HOME/bin/mopac.sh
> and the pdb was generated as can be seen from the attached file.
>
> Of course, I am now going to define again AMBERHOME as it was in my .bashrc. Do
> you believe that this may have other consequences than when using Amber score?

No.

Scott

> If not, I'll try to compile dock parallel.
>
> I could install DOCK as another user, though it makes everything less easy.
>
> Thanks
> francesco
>
> --- Scott Brozell <sbrozell at scripps.edu> wrote:
>
> > Hi,
> >
> > On Fri, 28 Sep 2007, Francesco Pietra wrote:
> >
> > > Yes, amberize_ligand failed and that was reflected on the other *.out
> > files.
> > > All three are attached.
> > >
> > > I can't foresee if Amber score  will become useful. Though, being somewhat
> > > familiar with Amber9, and having it, if there is any chance to fix this
> > problem
> > > ...
> > >
> > > To this regard, why was Antechamber calling divcon at
> > $AMBERHOME/bin/divcon?
> > > Which can't be found in DOCK. Divcon is available on my machine, though at
> > > $AMBERHOME/exe/divcon (where also antechamber is present).
> >
> > Ahh, this is a known problem that has been fixed in Amber/antechamber
> > land, but not yet released.
> > The patch is to undefine AMBERHOME and rerun the tests.
> >

From sbrozell at scripps.edu  Tue Oct  2 17:18:32 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Tue, 2 Oct 2007 17:18:32 -0700
Subject: [Dock-fans] dms install on Linux alongside Chimera and Dock6.1
In-Reply-To: <362655.23737.qm@web57602.mail.re1.yahoo.com>
References: <362655.23737.qm@web57602.mail.re1.yahoo.com>
Message-ID: <Pine.SGI.4.51.0710021710200.26335@pusar.scripps.edu>

Hi,

On Sun, 30 Sep 2007, Francesco Pietra wrote:

> I have installed (AS USER in Debian Linux amd64)
> AMBER9 and DOCK6.1 in:
> /usr/local/amber9
> /usr/local/dock6
>
> Serial and parallel tests for dock passed, though to use amber score I have to
> undefine AMBER. If not, Antechamber of dock calls divcon, which only exists in
> amber9 (known issue I learned).
>
> Then, on the same machine, I have installed (AS USER) dms (starting from
> dms.shar) in
> /usr/local/dms
> Is it possible to carry out tests for dms? Having scarce experience in

Try this tutorial:
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm

> Having scarce experience in
> compilations, I found a number of problems with dms. Editing GNUmakefile
> /usr/local/dms/lib (for LIBDIR)
> and
> /usr/local/dms/bin (for BINDIR)
> and creating such directories, was met with failure, contrary to expectations
> from the README: regular file '/usr/local/man/man1' can't be created.
> Therefore, I created such directories and further edited GNUmakefile as
> follows:
> PDBINC = /usr/local/dms/libpdb
> PDBLIB = /usr/local/dms/libpdb
> MANDIR = /usr/local/man/man1
> "make install" exited without error warnings.
>
> dms.1 is now located in
> /usr/local/dms/man/man1/dms.1
> and a "man" link was created:
> /usr/local/man/man1/man3
> where "man1" contains mpich++.1 mpicc.1.. etc and a link mpiCC.1, while "man3"
> contains various Troff documents, such as MPI.3 etc.
>
> I do not understand if this complex situation stems from a wrong editing of
> GNUmakefile.


It is not clear that there is a problem.
Does this file exist
/usr/local/dms/bin/dms
?
If so then you a dms executable which is probably all you need.

> I did nothing for parallelization. Is that easily feasible for my amd64 machine
> with shared memory?


Probably.

Scott

> I have installed Chimera 1,2422 on a Debain Linux i386 desktop scp linked to
> the above machine. The Chimera window opens, though I did not try to use it
> yet.

From Francis.Reyes at Colorado.EDU  Tue Oct  2 19:59:09 2007
From: Francis.Reyes at Colorado.EDU (Francis E Reyes)
Date: Tue, 2 Oct 2007 20:59:09 -0600
Subject: [Dock-fans] when dock6.mpi crashes....
Message-ID: <AC016C94-0331-4AD0-984C-8C1C17A1DE83@colorado.edu>

What steps can I do to restart where it left off? I understand I  
could use skip_molecule, but how about ranking, writing out conformers?

Thanks

FR

---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D



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From sbrozell at scripps.edu  Wed Oct  3 08:31:21 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Wed, 3 Oct 2007 08:31:21 -0700
Subject: [Dock-fans] when dock6.mpi crashes....
In-Reply-To: <AC016C94-0331-4AD0-984C-8C1C17A1DE83@colorado.edu>
References: <AC016C94-0331-4AD0-984C-8C1C17A1DE83@colorado.edu>
Message-ID: <Pine.SGI.4.51.0710030815360.26335@pusar.scripps.edu>

Hi,

On Tue, 2 Oct 2007, Francis E Reyes wrote:

> What steps can I do to restart where it left off? I understand I
> could use skip_molecule, but how about ranking, writing out conformers?

There is no restart facility yet; see these for past comments:
http://shoichetlab.compbio.ucsf.edu/pipermail/dock-fans/2007-August/001164.html
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-October/000750.html

Scott


From Francis.Reyes at Colorado.EDU  Wed Oct  3 09:09:35 2007
From: Francis.Reyes at Colorado.EDU (Francis E Reyes)
Date: Wed, 3 Oct 2007 10:09:35 -0600
Subject: [Dock-fans] when dock6.mpi crashes....
In-Reply-To: <Pine.SGI.4.51.0710030815360.26335@pusar.scripps.edu>
References: <AC016C94-0331-4AD0-984C-8C1C17A1DE83@colorado.edu>
	<Pine.SGI.4.51.0710030815360.26335@pusar.scripps.edu>
Message-ID: <D7E48CEB-915B-4568-8B55-42E4EDB7E408@colorado.edu>

How about writing conformers for all molecules that were ranked?

Are those now lost?

FR

---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D



On Oct 3, 2007, at 9:31 AM, Scott Brozell wrote:

> Hi,
>
> On Tue, 2 Oct 2007, Francis E Reyes wrote:
>
>> What steps can I do to restart where it left off? I understand I
>> could use skip_molecule, but how about ranking, writing out  
>> conformers?
>
> There is no restart facility yet; see these for past comments:
> http://shoichetlab.compbio.ucsf.edu/pipermail/dock-fans/2007-August/ 
> 001164.html
> http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-October/ 
> 000750.html
>
> Scott
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans

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From chiendarret at yahoo.com  Sun Oct  7 10:22:54 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Sun, 7 Oct 2007 10:22:54 -0700 (PDT)
Subject: [Dock-fans] Running interactive mode tutorials
Message-ID: <990872.29093.qm@web57612.mail.re1.yahoo.com>

I fear I am misunderstanding both tutorials and manual about commands in
interactive mode.

Using Dock6.1, I was unable to run interactively "Generating the Grid" tutorial
with command (grid.in nonexistent):

grid -i grid.in -o grid.out -s

By providing a hand generated grid.in with correct paths, the computation
completed successfully in 13 min.
________

Similarly, I was unable to run Docking tutorial with command (nonexistent
dock.in file):

mpirun -np 4 dock6.mpi -i dock.in

Error: DOCK must be run with the -o outfile option under MPI

Then, I tried:

mpirun -np 4 dock6.mpi -i dock.in -o dock.out

Initialing MPI Routines (for each cpu)
and  getting immediately four output files:

dock.out : Could not open vdw.defn.

Same problem with dock.out.# (# = 1, 2, 3)

Because the tutorial suggests to first generate the in file interactively in
view of heavy computations (my task), I am asking for help about my puzzle.

Thanks

francesco pietra


       
____________________________________________________________________________________
Yahoo! oneSearch: Finally, mobile search 
that gives answers, not web links. 
http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC

From Francis.Reyes at Colorado.EDU  Sun Oct  7 12:05:21 2007
From: Francis.Reyes at Colorado.EDU (Francis E Reyes)
Date: Sun, 7 Oct 2007 13:05:21 -0600
Subject: [Dock-fans] Running interactive mode tutorials
In-Reply-To: <990872.29093.qm@web57612.mail.re1.yahoo.com>
References: <990872.29093.qm@web57612.mail.re1.yahoo.com>
Message-ID: <562FB0D0-2F3A-430A-8567-3DD48F2D7B49@colorado.edu>

Does vdw.defn exist? Does it exist on all nodes?


FR
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D



On Oct 7, 2007, at 11:22 AM, Francesco Pietra wrote:

> I fear I am misunderstanding both tutorials and manual about  
> commands in
> interactive mode.
>
> Using Dock6.1, I was unable to run interactively "Generating the  
> Grid" tutorial
> with command (grid.in nonexistent):
>
> grid -i grid.in -o grid.out -s
>
> By providing a hand generated grid.in with correct paths, the  
> computation
> completed successfully in 13 min.
> ________
>
> Similarly, I was unable to run Docking tutorial with command  
> (nonexistent
> dock.in file):
>
> mpirun -np 4 dock6.mpi -i dock.in
>
> Error: DOCK must be run with the -o outfile option under MPI
>
> Then, I tried:
>
> mpirun -np 4 dock6.mpi -i dock.in -o dock.out
>
> Initialing MPI Routines (for each cpu)
> and  getting immediately four output files:
>
> dock.out : Could not open vdw.defn.
>
> Same problem with dock.out.# (# = 1, 2, 3)
>
> Because the tutorial suggests to first generate the in file  
> interactively in
> view of heavy computations (my task), I am asking for help about my  
> puzzle.
>
> Thanks
>
> francesco pietra
>
>
>
> ______________________________________________________________________ 
> ______________
> Yahoo! oneSearch: Finally, mobile search
> that gives answers, not web links.
> http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans

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From chiendarret at yahoo.com  Sun Oct  7 13:53:39 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Sun, 7 Oct 2007 13:53:39 -0700 (PDT)
Subject: [Dock-fans] Running interactive mode tutorials
In-Reply-To: <562FB0D0-2F3A-430A-8567-3DD48F2D7B49@colorado.edu>
Message-ID: <285317.7746.qm@web57608.mail.re1.yahoo.com>


--- Francis E Reyes <Francis.Reyes at Colorado.EDU> wrote:

> Does vdw.defn exist? Does it exist on all nodes?

/usr/local/dock6/parameters/vdw_AMBER_parm99.defn

which file is rw-r--r-- francesco francesco
________________
Then, I edited manually rigid.in (attached) and tried both parallel and serial


dock6.mpi -i dock.in -o dock.out

dock6 -i dock.in -o dock.out

getting same error:
Could not open vdw.defn for reading.

dock.out from serial command is also attached.
______________________
This

/usr/local/dock6/parameters/vdw_AMBER_parm99.defn

found no problems in "grid.in", tutorial "Generating the grid"


francesco


> FR
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
> 
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
> 
> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
> 
> 
> 
> On Oct 7, 2007, at 11:22 AM, Francesco Pietra wrote:
> 
> > I fear I am misunderstanding both tutorials and manual about  
> > commands in
> > interactive mode.
> >
> > Using Dock6.1, I was unable to run interactively "Generating the  
> > Grid" tutorial
> > with command (grid.in nonexistent):
> >
> > grid -i grid.in -o grid.out -s
> >
> > By providing a hand generated grid.in with correct paths, the  
> > computation
> > completed successfully in 13 min.
> > ________
> >
> > Similarly, I was unable to run Docking tutorial with command  
> > (nonexistent
> > dock.in file):
> >
> > mpirun -np 4 dock6.mpi -i dock.in
> >
> > Error: DOCK must be run with the -o outfile option under MPI
> >
> > Then, I tried:
> >
> > mpirun -np 4 dock6.mpi -i dock.in -o dock.out
> >
> > Initialing MPI Routines (for each cpu)
> > and  getting immediately four output files:
> >
> > dock.out : Could not open vdw.defn.
> >
> > Same problem with dock.out.# (# = 1, 2, 3)
> >
> > Because the tutorial suggests to first generate the in file  
> > interactively in
> > view of heavy computations (my task), I am asking for help about my  
> > puzzle.
> >
> > Thanks
> >
> > francesco pietra
> >
> >
> >
> > ______________________________________________________________________ 
> > ______________
> > Yahoo! oneSearch: Finally, mobile search
> > that gives answers, not web links.
> > http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> 
> 



       
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Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. 
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From chiendarret at yahoo.com  Sun Oct  7 14:40:36 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Sun, 7 Oct 2007 14:40:36 -0700 (PDT)
Subject: [Dock-fans] Running interactive mode tutorials
In-Reply-To: <562FB0D0-2F3A-430A-8567-3DD48F2D7B49@colorado.edu>
Message-ID: <854205.34262.qm@web57609.mail.re1.yahoo.com>

I have fixed the problem (at least by providing a prefabricated in file)

mpirun -np 4 dock6.mpi -i rigid.in -o rigid.out

Files are attached. Clearly, I did something silly before.

francesco

--- Francis E Reyes <Francis.Reyes at Colorado.EDU> wrote:

> Does vdw.defn exist? Does it exist on all nodes?
> 
> 
> FR
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
> 
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
> 
> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
> 
> 
> 
> On Oct 7, 2007, at 11:22 AM, Francesco Pietra wrote:
> 
> > I fear I am misunderstanding both tutorials and manual about  
> > commands in
> > interactive mode.
> >
> > Using Dock6.1, I was unable to run interactively "Generating the  
> > Grid" tutorial
> > with command (grid.in nonexistent):
> >
> > grid -i grid.in -o grid.out -s
> >
> > By providing a hand generated grid.in with correct paths, the  
> > computation
> > completed successfully in 13 min.
> > ________
> >
> > Similarly, I was unable to run Docking tutorial with command  
> > (nonexistent
> > dock.in file):
> >
> > mpirun -np 4 dock6.mpi -i dock.in
> >
> > Error: DOCK must be run with the -o outfile option under MPI
> >
> > Then, I tried:
> >
> > mpirun -np 4 dock6.mpi -i dock.in -o dock.out
> >
> > Initialing MPI Routines (for each cpu)
> > and  getting immediately four output files:
> >
> > dock.out : Could not open vdw.defn.
> >
> > Same problem with dock.out.# (# = 1, 2, 3)
> >
> > Because the tutorial suggests to first generate the in file  
> > interactively in
> > view of heavy computations (my task), I am asking for help about my  
> > puzzle.
> >
> > Thanks
> >
> > francesco pietra
> >
> >
> >
> > ______________________________________________________________________ 
> > ______________
> > Yahoo! oneSearch: Finally, mobile search
> > that gives answers, not web links.
> > http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> 
> 



       
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From chiendarret at yahoo.com  Mon Oct  8 02:34:05 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Mon, 8 Oct 2007 02:34:05 -0700 (PDT)
Subject: [Dock-fans] End graphical representation from Dock tutorials
Message-ID: <396115.10915.qm@web57610.mail.re1.yahoo.com>

I carried out all Dock6.1 tutorials with the aid of Chimera 1.2422 and DMS. The
relevant files used for, and got from, the flexible-ligand docking tutorial are
attached. I believe I used defaults. The out file attached is the one of the
four out files (from mpirun -np 4 ....) that seems to me to be relevant.

How to view graphically the best scored ligand from flex_scored.mole2 in the
protein? Just combine flex_scored.mole2 with the ligand-deprived receptor?

This in view of my project of looking for docking between a family of
lypophilic natural products (conformationally studied in vacuum with Amber9
simulated annealing) and a complex, large protein. I.e., by carrying out a
process of the type illustrated by the docking tutorial for each pocket of the
protein. I know there is interaction between the two (though a mere
disassembling of the lipid bilayer can't be rigorously ruled out yet) but no
idea where.



Thanks
francesco pietra


      ____________________________________________________________________________________
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From zzjsail at gmail.com  Mon Oct  8 10:55:26 2007
From: zzjsail at gmail.com (zzj)
Date: Mon, 8 Oct 2007 10:55:26 -0700
Subject: [Dock-fans] Dock-prep problem with Zn and K ions
Message-ID: <ad277c4c0710081055s54c96f62w386eedb91ddc3735@mail.gmail.com>

Hi there,
I am preparing dock6 files in Chimera using the Dockprep option. The
Zn and K ions in the PDB files are giving me problems at the point of
adding hydrogen. Everthing works fine if I remove these ion atoms.
Here is the Chimera Error message:
AttributeError: addHinfoDialog instance has no attribute "cancerlCB".
I can select and highlight these ions without problem. I tried to give
different names for the ions. Nothing worked.
Any suggestion is highly appreciated!
-Joe

From jinlian05 at lzu.cn  Thu Oct 11 05:06:23 2007
From: jinlian05 at lzu.cn (jinlian05 at lzu.cn)
Date: Thu, 11 Oct 2007 20:06:23 +0800
Subject: [Dock-fans] dock time?
Message-ID: <392104383.23487@st.lzu.edu.cn>

Hi:
I am a freshman to student DOCK6.0. I met some questions during using it.
The grid.nrg was about 30M, then i run dock6. But it has spent about 24 hours , it
is not end now. i dont know why??
Any suggestion is highly appreciated!



From sbrozell at scripps.edu  Thu Oct 11 07:55:22 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Thu, 11 Oct 2007 07:55:22 -0700
Subject: [Dock-fans] Anchor size and clashes elimination
In-Reply-To: <261159.6501.qm@web36707.mail.mud.yahoo.com>
References: <261159.6501.qm@web36707.mail.mud.yahoo.com>
Message-ID: <Pine.SGI.4.51.0710101406330.43300@pusar.scripps.edu>

Hi,

Here is an improved description of clash_overlap.
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#TimeRequirements

* use_clash_overlap [no] (yes, no):
  #Flag to check for overlapping atomic volumes during anchor and grow
      o clash_overlap [0.5] (float):
        #The relative threshold for overlapping atomic volumes;
        #a clash exists if the distance between a pair of atoms is less than
        #the clash_overlap times the sum of their atom type radii;
        #thus, a clash_overlap of 0.75 allows 25% (1 - 0.75) of relative overlap


Regarding worse docking with clash filtering than without,
the usual explanation is poor radii.

Scott


On Tue, 7 Aug 2007, Sudipto Mukherjee wrote:

Min Anchor size:
The default size of 40 atoms will cause Dock to select the largest anchor only for most molecules. Using a smaller anchor size rapidly increases the execution time though. min_anchor_size of 6  means the anchor can be as small as a single benzene ring. This parameter is somewhat analogous to the multiple_anchors parameter present in DOCK 4. Using multiple anchors can improve sampling in some cases, but mostly results in sampling similar conformers multiple times. Also, I would recommend using clustering when using a small min_anchor_size to prune the number of similar conformers sampled.

Clash_overlap:
DOCK computes clash overlap with the following formula:
if ( distance(atom_A, atom_B) < clash_overlap *( radius_atom_A + radius_atom_B ) ) assume there is a clash

See the segment_clash_check() function in conf_gen.ccp for details.

Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University


----- Original Message ----
From: Grzegorz Popowicz <popowicz at biochem.mpg.de>
To: dock-fans at docking.org
Sent: Monday, August 6, 2007 5:39:21 AM
Subject: [Dock-fans] Anchor size and clashes elimination

Hi all!
1. The default size of an anchor in DOCK is 40 atoms this generates quite  big
fragments as for beginning of docking (at least 480Da). I have tried smaller
anchors (8 atoms) with good results. Are there any rules governing selection
of anchor size?
2. Dock run with use_clash_overlap=no generates solutions with terrible
clashes (of course), however the predictions of known ligands binding are
very good in my case. With use_clash_overlap=yes and clash_overlap=0.5 (BTW.
What does percent of overlap mean?) there are no clushes but known ligands
are badly docked and scored much much worse than without clashes filter. Is
there any resonable explanation to this fact?


From sbrozell at scripps.edu  Thu Oct 11 08:10:03 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Thu, 11 Oct 2007 08:10:03 -0700
Subject: [Dock-fans] dock time?
In-Reply-To: <392104383.23487@st.lzu.edu.cn>
References: <392104383.23487@st.lzu.edu.cn>
Message-ID: <Pine.SGI.4.51.0710110800580.43300@pusar.scripps.edu>

Hi,

On Thu, 11 Oct 2007,  wrote:

> I am a freshman to student DOCK6.0. I met some questions during using it.
> The grid.nrg was about 30M, then i run dock6. But it has spent about 24 hours , it
> is not end now. i dont know why??
> Any suggestion is highly appreciated!

Since you didnt supply many clues,
the general advice is to run the tutorials
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm
and make incremental changes with plenty of trial runs.

Searching the archives
http://dock.compbio.ucsf.edu/DOCK_6/index.htm
with keywords such as, time or grid size finds:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-August/000679.html
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2005-May/000118.html

Scott


From sbrozell at scripps.edu  Thu Oct 11 11:43:19 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Thu, 11 Oct 2007 11:43:19 -0700
Subject: [Dock-fans] Dock-prep problem with Zn and K ions
In-Reply-To: <ad277c4c0710081055s54c96f62w386eedb91ddc3735@mail.gmail.com>
References: <ad277c4c0710081055s54c96f62w386eedb91ddc3735@mail.gmail.com>
Message-ID: <Pine.SGI.4.51.0710110812220.43300@pusar.scripps.edu>

Hi,

Resolved - old chimera was the problem:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-October/001892.html

Scott

On Mon, 8 Oct 2007, zzj wrote:

> I am preparing dock6 files in Chimera using the Dockprep option. The
> Zn and K ions in the PDB files are giving me problems at the point of
> adding hydrogen. Everthing works fine if I remove these ion atoms.
> Here is the Chimera Error message:
> AttributeError: addHinfoDialog instance has no attribute "cancerlCB".
> I can select and highlight these ions without problem. I tried to give
> different names for the ions. Nothing worked.
> Any suggestion is highly appreciated!

From sbrozell at scripps.edu  Thu Oct 11 12:37:07 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Thu, 11 Oct 2007 12:37:07 -0700
Subject: [Dock-fans] End graphical representation from Dock tutorials
In-Reply-To: <396115.10915.qm@web57610.mail.re1.yahoo.com>
References: <396115.10915.qm@web57610.mail.re1.yahoo.com>
Message-ID: <Pine.SGI.4.51.0710111145330.43300@pusar.scripps.edu>

Hi,

See
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-October/001889.html

An updated DOCK tutorial mentioning viewdock will be posted soon:
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/ligand_sampling_dock/ligand_sampling_dock.html

Scott

On Mon, 8 Oct 2007, Francesco Pietra wrote:

> I carried out all Dock6.1 tutorials with the aid of Chimera 1.2422 and DMS. The
> relevant files used for, and got from, the flexible-ligand docking tutorial are
> attached. I believe I used defaults. The out file attached is the one of the
> four out files (from mpirun -np 4 ....) that seems to me to be relevant.
>
> How to view graphically the best scored ligand from flex_scored.mole2 in the
> protein? Just combine flex_scored.mole2 with the ligand-deprived receptor?
>
> This in view of my project of looking for docking between a family of
> lypophilic natural products (conformationally studied in vacuum with Amber9
> simulated annealing) and a complex, large protein. I.e., by carrying out a
> process of the type illustrated by the docking tutorial for each pocket of the
> protein. I know there is interaction between the two (though a mere
> disassembling of the lipid bilayer can't be rigorously ruled out yet) but no
> idea where.

From chiendarret at yahoo.com  Thu Oct 11 22:45:17 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Thu, 11 Oct 2007 22:45:17 -0700 (PDT)
Subject: [Dock-fans] Model of lipid bilayer for docking
Message-ID: <494579.12060.qm@web57613.mail.re1.yahoo.com>

I have raised a discussion on the tools available for building lipid bilayers.

In that context I suppose that phosphatidylcholine- or
polyenylphosphatidylcholine-based bilayers are computationally very costly.
Under the presumption that octane-water models of  lipid bilayer involve much
less computational cost, are they a promising initial route in the exploration
if there is any docking at all with complicated - non polymeric - potential
ligands? Also, are there examples of docking using more advanced models of
lipid bilayer?

Separately I have asked is complex bilayers built with VMD are transferable to
the Amber-Dock-Chimera world.

Thanks
francesco pietra 


       
____________________________________________________________________________________
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From chiendarret at yahoo.com  Sat Oct 13 09:57:52 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Sat, 13 Oct 2007 09:57:52 -0700 (PDT)
Subject: [Dock-fans] Fwd: Model of lipid bilayer for docking
Message-ID: <834996.22054.qm@web57607.mail.re1.yahoo.com>

I am posting again because on the Chimera list - in the context of a related
question - I was advised to possibly strip out the lipid bilayer before going
to Dock from Amber.

Though, I have seen recently a docking study (GOLD 3.0) with a membrane
protein, where the authors carefully immersed the protein in a thick layer of
octane and then the whole was solvated with water.

I would be grateful for advice about.

Thanks
francesco

--- Francesco Pietra <chiendarret at yahoo.com> wrote:

> Date: Thu, 11 Oct 2007 22:45:17 -0700 (PDT)
> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: Model of lipid bilayer for docking
> To: dock-fans <dock-fans at docking.org>
> 
> I have raised a discussion on the tools available for building lipid
> bilayers.
> 
> In that context I suppose that phosphatidylcholine- or
> polyenylphosphatidylcholine-based bilayers are computationally very costly.
> Under the presumption that octane-water models of  lipid bilayer involve much
> less computational cost, are they a promising initial route in the
> exploration
> if there is any docking at all with complicated - non polymeric - potential
> ligands? Also, are there examples of docking using more advanced models of
> lipid bilayer?
> 
> Separately I have asked is complex bilayers built with VMD are transferable
> to
> the Amber-Dock-Chimera world.
> 
> Thanks
> francesco pietra 
> 
> 
>        
>
____________________________________________________________________________________
> Need a vacation? Get great deals
> to amazing places on Yahoo! Travel.
> http://travel.yahoo.com/
> 



       
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From sudmukh at yahoo.com  Mon Oct 15 08:35:53 2007
From: sudmukh at yahoo.com (Sudipto Mukherjee)
Date: Mon, 15 Oct 2007 08:35:53 -0700 (PDT)
Subject: [Dock-fans] Model of lipid bilayer for docking
Message-ID: <643873.29095.qm@web36707.mail.mud.yahoo.com>

Francesco,

VMD can create MOL2 files. Save your membrane model as a MOL2 file; make sure it has charges. DOCK should work fine.
You can then use this MOL2 file to create a grid and spheres to proceed with docking. 
Singlepoint continuous scoring should also work, though Dock can take several minutes to score a receptor which includes a large membrane.

Docking does not do very well with large, non-druglike ligands. If your ligands have a lot of rotatable bonds, DOCK may face problems.
 
Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University
Lab: 631-632-8519, Mobile: 631-220-5744


----- Original Message ----
From: Francesco Pietra <chiendarret at yahoo.com>
To: dock-fans <dock-fans at docking.org>
Sent: Friday, October 12, 2007 1:45:17 AM
Subject: [Dock-fans] Model of lipid bilayer for docking


I have raised a discussion on the tools available for building lipid
 bilayers.

In that context I suppose that phosphatidylcholine- or
polyenylphosphatidylcholine-based bilayers are computationally very
 costly.
Under the presumption that octane-water models of  lipid bilayer
 involve much
less computational cost, are they a promising initial route in the
 exploration
if there is any docking at all with complicated - non polymeric -
 potential
ligands? Also, are there examples of docking using more advanced models
 of
lipid bilayer?

Separately I have asked is complex bilayers built with VMD are
 transferable to
the Amber-Dock-Chimera world.

Thanks
francesco pietra 


       
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Dock-fans at docking.org
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From lujing1999 at 126.com  Tue Oct 16 23:09:03 2007
From: lujing1999 at 126.com (=?gb2312?Q?=C2=B9=BE=A7jinger.Lu?=)
Date: Wed, 17 Oct 2007 14:09:03 +0800 (CST)
Subject: [Dock-fans] score.o error1
Message-ID: <4715A6FF.000093.04421@bj126app15.126.com>

Hi, dock-fans , I am trying to install dock6.1 in linux and  having some problems. After configuring with gnu and using the "make all" command, the installation runs for a  bit.  Then some error messages appear. The folowwing is the complete output from make all. 
 
 
Starting installation of 
DOCK v6.1
at Wed Oct 17 11:55:53 CST 2007.
cd ../src && make install
make[1]: Entering directory `/home/qlli/tmp/dock6/src'
cd dock && make install
make[2]: Entering directory `/home/qlli/tmp/dock6/src/dock'
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o amber_typer.o  amber_typer.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o base_mpi.o  base_mpi.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o base_score.o  base_score.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o conf_gen.o  conf_gen.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o dock.o  dock.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o dockmol.o  dockmol.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o library_file.o  library_file.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o master_score.o  master_score.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o orient.o  orient.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o score.o  score.cpp
score.cpp: In method `string Energy_Score::output_score_summary 
(float)':
score.cpp:407: `fixed' undeclared (first use this function)
score.cpp:407: (Each undeclared identifier is reported only once for 
each function it appears in.)
make[2]: *** [score.o] Error 1
make[2]: Leaving directory `/home/qlli/tmp/dock6/src/dock'
make[1]: *** [dock6] Error 2
make[1]: Leaving directory `/home/qlli/tmp/dock6/src'
make: *** [install] Error 2

 
 
Thanks for your time and help.--
jinger.Lu
TEL:13488692141
QQ: 58187898
MSN:zhishang_feng at hotmail.com
email:lujing1999 at 126.com

 
 
 
 



? ? ? ? ? ? ? ?? ? ? ? ? ? ? ? ? ? ?? ? ? ? >> 
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From sudmukh at yahoo.com  Wed Oct 17 08:19:31 2007
From: sudmukh at yahoo.com (Sudipto Mukherjee)
Date: Wed, 17 Oct 2007 08:19:31 -0700 (PDT)
Subject: [Dock-fans] score.o error1
Message-ID: <351657.579.qm@web36712.mail.mud.yahoo.com>

Dear Lu,

Looks like you are trying to compile dock with mpi. Did you face the same issue while compiling a serial version of dock?
 
Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University

----- Original Message ----
From: ??jinger.Lu <lujing1999 at 126.com>
To: dock-fans at docking.org
Sent: Wednesday, October 17, 2007 2:09:03 AM
Subject: [Dock-fans] score.o error1


Hi, dock-fans , I am trying to install dock6.1 in linux and  having some problems. After configuring with gnu and using the "make all" command, the installation runs for a  bit.  Then some error messages appear. The folowwing is the complete output from make all. 

 

 

Starting installation of 
DOCK v6.1
at Wed Oct 17 11:55:53 CST 2007.

cd ../src && make install
make[1]: Entering directory `/home/qlli/tmp/dock6/src'
cd dock && make install
make[2]: Entering directory `/home/qlli/tmp/dock6/src/dock'
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o amber_typer.o  amber_typer.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o base_mpi.o  base_mpi.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o base_score.o  base_score.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o conf_gen.o  conf_gen.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o dock.o  dock.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o dockmol.o  dockmol.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o library_file.o  library_file.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o master_score.o  master_score.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o orient.o  orient.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o score.o  score.cpp
score.cpp: In method `string Energy_Score::output_score_summary 
(float)':
score.cpp:407: `fixed' undeclared (first use this function)
score.cpp:407: (Each undeclared identifier is reported only once for 
each function it appears in.)
make[2]: *** [score.o] Error 1
make[2]: Leaving directory `/home/qlli/tmp/dock6/src/dock'
make[1]: *** [dock6] Error 2
make[1]: Leaving directory `/home/qlli/tmp/dock6/src'
make: *** [install] Error 2


 

 

Thanks for your time and help.
--
jinger.Lu
TEL:13488692141
QQ: 58187898
MSN:zhishang_feng at hotmail.com
email:lujing1999 at 126.com

 

 

 

 





? ? ? ? ? ? ? ?? ? ? ? ? ? ? ? ? ? ?? ? ? ? >> 




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From chiendarret at yahoo.com  Thu Oct 18 07:47:48 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Thu, 18 Oct 2007 07:47:48 -0700 (PDT)
Subject: [Dock-fans] dms on the PATH
Message-ID: <426839.90750.qm@web57602.mail.re1.yahoo.com>

Is it an env variable to put dms on the user's .bashrc so that to have dms on
the PATH?

Thanks
francesco pietra

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
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From chiendarret at yahoo.com  Thu Oct 18 09:38:37 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Thu, 18 Oct 2007 09:38:37 -0700 (PDT)
Subject: [Dock-fans] generatin Sphere failure
Message-ID: <730885.8420.qm@web57601.mail.re1.yahoo.com>

I carried out successfully all DOCK6.1 tutorials. In contrast, when I tried to
apply the defaults of the tutorials to a large protein (an ion channel teepee),
I met failure at the Generating Spheres stage.

Command "sphgen" generated an empty teepee_noH.sph  file (the requested file in
INSPH), alongside temp1.ms temp2.sph temp3.atc files. The error is illustrated
in OUTSPH:

density type = X
 reading  teepee_noH.ms                                                        
         type   R
 # of atoms =   3412   # of surf pts =  *****
 finding spheres for   teepee_noH.ms                                           
                   
 dotlim =     0.000
 radmax =    4.000
 Minimum radius of acceptable spheres?
  1.39999998
 output to  teepee_noH.sph                                                     
        
 error reading temp2.sph
    0   89  1.4954  100457    0.011160   25.497364   11.149721  -10.546585


There are no "# of surf pts" and "temp2.sph" could not be read. Was that due to
a too large protein or to unsuited defaults of the tutorial? Also, are the
temp.* files intermediate files during the computation? (they were not present
at completed tutorial). I can't imagine if this is sufficient information for a
rough diagnosis. It is the first time I move outside the tutorials with DOCK.

Thanks

francesco pietra



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From sbrozell at scripps.edu  Thu Oct 18 09:54:38 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Thu, 18 Oct 2007 09:54:38 -0700
Subject: [Dock-fans] dms on the PATH
In-Reply-To: <426839.90750.qm@web57602.mail.re1.yahoo.com>
References: <426839.90750.qm@web57602.mail.re1.yahoo.com>
Message-ID: <Pine.SGI.4.51.0710180929050.57099@pusar.scripps.edu>

Hi,

On Thu, 18 Oct 2007, Francesco Pietra wrote:

> Is it an env variable to put dms on the user's .bashrc so that to have dms on
> the PATH?

Just use PATH itself:
PATH=/bla/dms:$PATH

or copy /bla/dms/dms into something already in your PATH, e.g.:
cp /bla/dms/dms $DOCK_HOME/bin

Scott


From sbrozell at scripps.edu  Thu Oct 18 10:00:46 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Thu, 18 Oct 2007 10:00:46 -0700
Subject: [Dock-fans] score.o error1
In-Reply-To: <351657.579.qm@web36712.mail.mud.yahoo.com>
References: <351657.579.qm@web36712.mail.mud.yahoo.com>
Message-ID: <Pine.SGI.4.51.0710180954510.57099@pusar.scripps.edu>

Hi,

fixed is a member of the C++ standard library.
Perhaps you have a really old g++, i.e., pre 3.0 ?

And as Sudipto indicates, start with a serial install.
Your config.h was definitely not produced via
cd install
./configure gnu

Scott

On Wed, 17 Oct 2007, Sudipto Mukherjee wrote:

> Looks like you are trying to compile dock with mpi. Did you face the same issue while compiling a serial version of dock?

----- Original Message ----
From: ????jinger.Lu <lujing1999 at 126.com>
To: dock-fans at docking.org
Sent: Wednesday, October 17, 2007 2:09:03 AM
Subject: [Dock-fans] score.o error1


Hi, dock-fans , I am trying to install dock6.1 in linux and  having some problems. After configuring with gnu and using the "make all" command, the installation runs for a  bit.  Then some error messages appear. The folowwing is the complete output from make all.

Starting installation of
DOCK v6.1
at Wed Oct 17 11:55:53 CST 2007.

cd ../src && make install
make[1]: Entering directory `/home/qlli/tmp/dock6/src'
cd dock && make install
make[2]: Entering directory `/home/qlli/tmp/dock6/src/dock'
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o amber_typer.o  amber_typer.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o base_mpi.o  base_mpi.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o base_score.o  base_score.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o conf_gen.o  conf_gen.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o dock.o  dock.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o dockmol.o  dockmol.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o library_file.o  library_file.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o master_score.o  master_score.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o orient.o  orient.cpp
g++ -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/home/qlli/qlli/Applications/mpich-1.2.7/include -O2 -o score.o  score.cpp
score.cpp: In method `string Energy_Score::output_score_summary
(float)':
score.cpp:407: `fixed' undeclared (first use this function)
score.cpp:407: (Each undeclared identifier is reported only once for
each function it appears in.)
make[2]: *** [score.o] Error 1
make[2]: Leaving directory `/home/qlli/tmp/dock6/src/dock'
make[1]: *** [dock6] Error 2

From osmany_guirola at yahoo.com  Thu Oct 18 15:03:21 2007
From: osmany_guirola at yahoo.com (Osmany Guirola)
Date: Thu, 18 Oct 2007 15:03:21 -0700 (PDT)
Subject: [Dock-fans] Calcium  problem with amber score
Message-ID: <575569.63737.qm@web43131.mail.sp1.yahoo.com>

Hi Fans
I am trying to use the amber score but i am having problems with
the prepare_amberize.pl script...my pdb file has a Ca ion and this is the error in the log file

For atom: .R<CA 45>.A<CA 1> Could not find type: Ca
Parameter file was not saved.
        Quit

of course my rec*.prmtop files have 0kb size
what can i do?





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From chiendarret at yahoo.com  Fri Oct 19 10:48:55 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Fri, 19 Oct 2007 10:48:55 -0700 (PDT)
Subject: [Dock-fans] Fwd: generatin Sphere failure
Message-ID: <269133.36725.qm@web57614.mail.re1.yahoo.com>

I solved the problem with Andrew Magis' sphgen_cpp 

francesco

--- Francesco Pietra <chiendarret at yahoo.com> wrote:

> Date: Thu, 18 Oct 2007 09:38:37 -0700 (PDT)
> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: generating Sphere failure
> To: dock-fans <dock-fans at docking.org>
> 
> I carried out successfully all DOCK6.1 tutorials. In contrast, when I tried
> to
> apply the defaults of the tutorials to a large protein (an ion channel
> teepee),
> I met failure at the Generating Spheres stage.
> 
> Command "sphgen" generated an empty teepee_noH.sph  file (the requested file
> in
> INSPH), alongside temp1.ms temp2.sph temp3.atc files. The error is
> illustrated
> in OUTSPH:
> 
> density type = X
>  reading  teepee_noH.ms                                                      
>  
>          type   R
>  # of atoms =   3412   # of surf pts =  *****
>  finding spheres for   teepee_noH.ms                                         
>  
>                    
>  dotlim =     0.000
>  radmax =    4.000
>  Minimum radius of acceptable spheres?
>   1.39999998
>  output to  teepee_noH.sph                                                   
>  
>         
>  error reading temp2.sph
>     0   89  1.4954  100457    0.011160   25.497364   11.149721  -10.546585
> 
> 
> There are no "# of surf pts" and "temp2.sph" could not be read. Was that due
> to
> a too large protein or to unsuited defaults of the tutorial? Also, are the
> temp.* files intermediate files during the computation? (they were not
> present
> at completed tutorial). I can't imagine if this is sufficient information for
> a
> rough diagnosis. It is the first time I move outside the tutorials with DOCK.
> 
> Thanks
> 
> francesco pietra
> 
> 
> 
> __________________________________________________
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From chiendarret at yahoo.com  Sun Oct 21 09:45:19 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Sun, 21 Oct 2007 09:45:19 -0700 (PDT)
Subject: [Dock-fans] Unbiased docking
In-Reply-To: <Pine.SGI.4.51.0709281223580.10676@pusar.scripps.edu>
Message-ID: <849495.84468.qm@web57614.mail.re1.yahoo.com>

Based on the suggestions below, I have followed the layout and settings of the
Dock6.1-web-page tutorials for my model pore protein (3400 heavy atoms, noH, no
solvent added) and 150-atoms neutral, lipidic ligand (bearing all hydrogens),
using the minimum energy conformation of the latter from Amber9 simulated
annealing in vacuum.

sphgen failed, while sphgen_cpp built re.ms and rec.sph in a few minutes,
118807 surface points in 91 clusters. I was surprised to see roughly the same
sphere distribution for clusters # 1, 2, and 91. Hope that sounds correct. I
did not examine other clusters, and all was done very roughly at the open eye.

Grid OK in ca 1h and half.

Rigid docking completed in 5 min wall time, showing the elongated ligand (made
of annealed rings) inside the cone, with the head out. Grid score -52.3.

Flex docking (cpu time ca 3h; anchors 1; orientations 500, conformations 115,
grid score -69.2, vdw -67.2, es -2). The arrangement of the ligand within the
pore was roughly the same as for rigid  docking, through the head of the ligand
was docked differently.

I did not carry out any docking with higher-energy conformers of the ligand.

This long story because it is the first time I am at docking outside tutorials,
to hopefully get suggestions as to go on. I could either carry out amber score,
and the relevant tutorial I have found outside the dock web page is clear
enough. Is that what Scott had in mind when he kindly suggested "go to Amber
after docking, and with the MD results back to Dock" or should I rather skip
amber scoring and go directly to Amber 9 to carry out a regular MD, may be with
the pore model inside POPC? If so, which is the shortest way to use my above
results from DOCK to set up the Amber 9 MD? (I mean, how to save the pore
protein plus the ligand so that Amber 9 can work; I am familiar with prmtop and
inprc file, while I read that Amber 9 can't import mol2 files with more than
one residue; if I save protein+ligand as pdb, how to get parameters for the
ligand? Or, if I save the protein and ligand separately do they conserve their
respective positions?.

Thanks

francesco



--- Scott Brozell <sbrozell at scripps.edu> wrote:

> Hi,
> 
> On Fri, 28 Sep 2007, Francesco Pietra wrote:
> 
> > Although not yet ready with DOCK6.1 installation, inspection of tutorials
> > prompts a couple of questions that may help planning.
> >
> > What I want to do at the moment is verifying if there is docking at all
> between
> > a family of natural products and a complicated protein. Not in a bilayer
> for
> > the moment.
> >
> > I have already carried out a conformational search for my natural products
> by
> > simulated annealing with an algorithm that calls Amber9. Parameter and
> > coordinate files for Amber9 were built with Antechamber/Divcon (ie AM1).
> >
> > The tutorial on DOCK web site starts from a protein-ligand complex, ie from
> a
> > definite receptor site in the protein. Is any graphical or alphanumeric
> > tutorial for the unbiased docking I am aimed at?
> 
> Not that I am aware of.
> There is a lot of flexibility in binding sites selection;
> see step 3 of
>
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm
> If your complicated protein is big then that may put a practical limit
> on the size of your grid; one approach would be to divide and conquer
> the big protein binding sites into subsets that would be processed
> separately.
> Perhaps others have comments ?
> 
> > DOCK6.1 is being compiled on a parallel amd64 machine (Debian Linux amd64
> with
> > 4GB RAM per cpu, ie a machine better suited for ab initio calculations than
> > classical MD), where also Amber9 is installed. Although the X system exists
> (in
> > fact, xleap requires it) and even Gnome could be called, the machine is
> > normally used with X killed. I manage anything graphical for Amber9 (to the
> > exception of xleap) on a single-Athlon desktop (Debian Linux i386 etch).
> The
> > two machines are scp linked, which is the way I exchange files between the
> two
> > machines.
> >
> > At 32bit I (1) prepare pdb files for "small molecules" with a MM package;
> (2)
> > examine everything graphical with VMD.
> >
> > On these basis, where to install Chimera for DOCK? I noticed that Chimera
> calls
> > both Dock Prep and Antechamber.
> 
> 
> Installing Chimera on the same machine as VMD seems reasonable.
> Any textual input and output files can be communicated between the machines.
> 
> > Similarly, where to install dms for DOCK?
> 
> dms is small.  I install it in my dock directory.
> 
> 
> > I understand that these are generic question, normally not for mailing
> lists.
> > Though, a couple of suggestions would greatly help me (an organic chemist,
> just
> > now beginning to touch the area of the biochemist) in the high complexity
> of
> > the docking affairs.
> 
> 
> This is the best place for all questions.
> 
> Scott
> 
> 


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From chiendarret at yahoo.com  Mon Oct 22 13:37:01 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Mon, 22 Oct 2007 13:37:01 -0700 (PDT)
Subject: [Dock-fans] Long bonds
Message-ID: <79669.97240.qm@web57607.mail.re1.yahoo.com>

With my large protein and ligand I was able to carry out docking, both rigid
and flex ligand. Amber_score failed because of two kinds of problems with the
protein.

1st PROBLEM (protons on histidine, etc): 
FATAL:  Atom .R<GLU 443>.A<HE1 16> does not have a type.
FATAL:  Atom .R<HIE 441>.A<HD1 18> does not have a type.
FATAL:  Atom .R<ASP 402>.A<HD1 13> does not have a type.
FATAL:  Atom .R<ASP 386>.A<HD1 13> does not have a type.
FATAL:  Atom .R<HIE 380>.A<HD1 18> does not have a type.
FATAL:  Atom .R<ASP 375>.A<HD1 13> does not have a type.
FATAL:  Atom .R<GLU 373>.A<HE1 16> does not have a type.
FATAL:  Atom .R<GLU 332>.A<HE1 16> does not have a type.
FATAL:  Atom .R<HIE 330>.A<HD1 18> does not have a type.
FATAL:  Atom .R<ASP 291>.A<HD1 13> does not have a type.
FATAL:  Atom .R<ASP 275>.A<HD1 13> does not have a type.
FATAL:  Atom .R<HIE 269>.A<HD1 18> does not have a type.
FATAL:  Atom .R<ASP 264>.A<HD1 13> does not have a type.
FATAL:  Atom .R<GLU 262>.A<HE1 16> does not have a type.
FATAL:  Atom .R<GLU 221>.A<HE1 16> does not have a type.
FATAL:  Atom .R<HIE 219>.A<HD1 18> does not have a type.
FATAL:  Atom .R<ASP 180>.A<HD1 13> does not have a type.
FATAL:  Atom .R<ASP 164>.A<HD1 13> does not have a type.
FATAL:  Atom .R<HIE 158>.A<HD1 18> does not have a type.
FATAL:  Atom .R<ASP 153>.A<HD1 13> does not have a type.
FATAL:  Atom .R<GLU 151>.A<HE1 16> does not have a type.
FATAL:  Atom .R<GLU 128>.A<HE1 16> does not have a type.
FATAL:  Atom .R<GLU 110>.A<HE1 16> does not have a type.
FATAL:  Atom .R<HIE 108>.A<HD1 18> does not have a type.
FATAL:  Atom .R<ASP 69>.A<HD1 13> does not have a type.
FATAL:  Atom .R<ASP 53>.A<HD1 13> does not have a type.
FATAL:  Atom .R<HIE 47>.A<HD1 18> does not have a type.
FATAL:  Atom .R<ASP 42>.A<HD1 13> does not have a type.
FATAL:  Atom .R<GLU 40>.A<HE1 16> does not have a type.
FATAL:  Atom .R<GLU 17>.A<HE1 16> does not have a type.
FATAL:  Atom .R<NSER 1>.A<H 14> does not have a type.

Is that better in such cases to edit the names by hand (problematic with
aspartic, H on O), or make recourse to (a) downlodable sourceforge softw, (b)
"biophysics" softw on server?

----------------------------

2nd PROBLEM:

WARNING: There is a bond of 50.040630 angstroms between: 
-------  .R<THR 333>.A<C 13> and .R<SER 334>.A<N 1>
WARNING: There is a bond of 39.464740 angstroms between: 
-------  .R<THR 222>.A<C 13> and .R<SER 223>.A<N 1>
WARNING: There is a bond of 49.372740 angstroms between: 

I was advised to insert "TER" records between the residues that the bond is
connecting. For the first long bond, is that correct as follows:

ATOM   5140  N   THR X 333      13.448 -15.558  22.741  0.00  0.00            
ATOM   5141  H   THR X 333      12.608 -15.012  22.643  0.00  0.00            
ATOM   5142  CA  THR X 333      14.691 -14.863  22.954  0.00  0.00            
ATOM   5143  HA  THR X 333      15.655 -15.355  22.580  0.00  0.00            
ATOM   5144  CB  THR X 333      14.648 -13.582  22.114  0.00  0.00            
ATOM   5145  HB  THR X 333      15.582 -13.069  22.291  0.00  0.00            
ATOM   5146  CG2 THR X 333      14.455 -13.769  20.605  0.00  0.00            
ATOM   5147 HG21 THR X 333      14.158 -12.806  20.145  0.00  0.00            
ATOM   5148 HG22 THR X 333      15.321 -14.161  20.049  0.00  0.00            
ATOM   5149 HG23 THR X 333      13.626 -14.520  20.409  0.00  0.00            
ATOM   5150  OG1 THR X 333      13.670 -12.723  22.556  0.00  0.00            
ATOM   5151  HG1 THR X 333      12.831 -13.194  22.522  0.00  0.00            
ATOM   5152  C   THR X 333      14.755 -14.634  24.443  0.00  0.00            
ATOM   5153  O   THR X 333      15.694 -15.150  25.132  0.00  0.00 
TER           
ATOM   5154  N   SER X 334     -16.176  22.312  10.940  0.00  0.00            
ATOM   5155  H   SER X 334     -15.301  22.760  10.966  0.00  0.00            
ATOM   5156  CA  SER X 334     -16.224  20.932  11.429  0.00  0.00            
ATOM   5157  HA  SER X 334     -17.198  20.770  11.905  0.00  0.00            
ATOM   5158  CB  SER X 334     -15.868  19.959  10.306  0.00  0.00            
ATOM   5159  HB2 SER X 334     -15.761  18.918  10.709  0.00  0.00            
ATOM   5160  HB3 SER X 334     -14.903  20.280   9.956  0.00  0.00            
ATOM   5161  OG  SER X 334     -16.906  19.973   9.300  0.00  0.00            
ATOM   5162  HG  SER X 334     -16.948  20.844   8.983  0.00  0.00            
ATOM   5163  C   SER X 334     -15.185  20.856  12.533  0.00  0.00            
ATOM   5164  O   SER X 334     -14.212  21.643  12.566  0.00  0.00 

Thanks
francesco pietra  

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From chiendarret at yahoo.com  Mon Oct 22 13:48:40 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Mon, 22 Oct 2007 13:48:40 -0700 (PDT)
Subject: [Dock-fans] Fwd: Long bonds
Message-ID: <32221.9540.qm@web57611.mail.re1.yahoo.com>

Sorry, forgot: how to recognize where the protons are on histidine, so that HIE
can be changed to HID? Similarly for aspartic.

--- Francesco Pietra <chiendarret at yahoo.com> wrote:

> Date: Mon, 22 Oct 2007 13:37:01 -0700 (PDT)
> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: Long bonds
> To: dock-fans <dock-fans at docking.org>
> 
> With my large protein and ligand I was able to carry out docking, both rigid
> and flex ligand. Amber_score failed because of two kinds of problems with the
> protein.
> 
> 1st PROBLEM (protons on histidine, etc): 
> FATAL:  Atom .R<GLU 443>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<HIE 441>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 402>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<ASP 386>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<HIE 380>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 375>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<GLU 373>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<GLU 332>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<HIE 330>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 291>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<ASP 275>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<HIE 269>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 264>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<GLU 262>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<GLU 221>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<HIE 219>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 180>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<ASP 164>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<HIE 158>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 153>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<GLU 151>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<GLU 128>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<GLU 110>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<HIE 108>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 69>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<ASP 53>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<HIE 47>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 42>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<GLU 40>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<GLU 17>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<NSER 1>.A<H 14> does not have a type.
> 
> Is that better in such cases to edit the names by hand (problematic with
> aspartic, H on O), or make recourse to (a) downlodable sourceforge softw, (b)
> "biophysics" softw on server?
> 
> ----------------------------
> 
> 2nd PROBLEM:
> 
> WARNING: There is a bond of 50.040630 angstroms between: 
> -------  .R<THR 333>.A<C 13> and .R<SER 334>.A<N 1>
> WARNING: There is a bond of 39.464740 angstroms between: 
> -------  .R<THR 222>.A<C 13> and .R<SER 223>.A<N 1>
> WARNING: There is a bond of 49.372740 angstroms between: 
> 
> I was advised to insert "TER" records between the residues that the bond is
> connecting. For the first long bond, is that correct as follows:
> 
> ATOM   5140  N   THR X 333      13.448 -15.558  22.741  0.00  0.00           
> 
> ATOM   5141  H   THR X 333      12.608 -15.012  22.643  0.00  0.00           
> 
> ATOM   5142  CA  THR X 333      14.691 -14.863  22.954  0.00  0.00           
> 
> ATOM   5143  HA  THR X 333      15.655 -15.355  22.580  0.00  0.00           
> 
> ATOM   5144  CB  THR X 333      14.648 -13.582  22.114  0.00  0.00           
> 
> ATOM   5145  HB  THR X 333      15.582 -13.069  22.291  0.00  0.00           
> 
> ATOM   5146  CG2 THR X 333      14.455 -13.769  20.605  0.00  0.00           
> 
> ATOM   5147 HG21 THR X 333      14.158 -12.806  20.145  0.00  0.00           
> 
> ATOM   5148 HG22 THR X 333      15.321 -14.161  20.049  0.00  0.00           
> 
> ATOM   5149 HG23 THR X 333      13.626 -14.520  20.409  0.00  0.00           
> 
> ATOM   5150  OG1 THR X 333      13.670 -12.723  22.556  0.00  0.00           
> 
> ATOM   5151  HG1 THR X 333      12.831 -13.194  22.522  0.00  0.00           
> 
> ATOM   5152  C   THR X 333      14.755 -14.634  24.443  0.00  0.00           
> 
> ATOM   5153  O   THR X 333      15.694 -15.150  25.132  0.00  0.00 
> TER           
> ATOM   5154  N   SER X 334     -16.176  22.312  10.940  0.00  0.00           
> 
> ATOM   5155  H   SER X 334     -15.301  22.760  10.966  0.00  0.00           
> 
> ATOM   5156  CA  SER X 334     -16.224  20.932  11.429  0.00  0.00           
> 
> ATOM   5157  HA  SER X 334     -17.198  20.770  11.905  0.00  0.00           
> 
> ATOM   5158  CB  SER X 334     -15.868  19.959  10.306  0.00  0.00           
> 
> ATOM   5159  HB2 SER X 334     -15.761  18.918  10.709  0.00  0.00           
> 
> ATOM   5160  HB3 SER X 334     -14.903  20.280   9.956  0.00  0.00           
> 
> ATOM   5161  OG  SER X 334     -16.906  19.973   9.300  0.00  0.00           
> 
> ATOM   5162  HG  SER X 334     -16.948  20.844   8.983  0.00  0.00           
> 
> ATOM   5163  C   SER X 334     -15.185  20.856  12.533  0.00  0.00           
> 
> ATOM   5164  O   SER X 334     -14.212  21.643  12.566  0.00  0.00 
> 
> Thanks
> francesco pietra  
> 
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around 
> http://mail.yahoo.com 
> 


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From burgosgu at ualberta.ca  Fri Oct 26 14:16:58 2007
From: burgosgu at ualberta.ca (burgosgu at ualberta.ca)
Date: Fri, 26 Oct 2007 15:16:58 -0600
Subject: [Dock-fans] Fixing protonation state
Message-ID: <20071026151658.akhue00740s44ss0@webmail.ualberta.ca>

Hi everybody,

I need to have a compound correctly protonated to dock it. I tried to  
use the resource of
"upload sets" of ZINC, but it seems that it does not have the required  
charactersitics of
bioavailability and non-toxicity, because it gives me no output as it  
did with other
compounds.

The smile for this compound is:
C1=C(C=CC2=C1C(=C[N]2)CC(=O)NCCCNCCCCNCCCNC(=O)CC3=C[N]C4=C3C=C(C=C4)Br)Br

Any suggestions??

THANKS,

Asdrubal


From sbrozell at scripps.edu  Fri Oct 26 17:04:14 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Fri, 26 Oct 2007 17:04:14 -0700 (PDT)
Subject: [Dock-fans] Fixing protonation state
In-Reply-To: <20071026151658.akhue00740s44ss0@webmail.ualberta.ca>
Message-ID: <Pine.LNX.4.44.0710261657330.12022-100000@loyd.scripps.edu>

Hi,

On Fri, 26 Oct 2007 burgosgu at ualberta.ca wrote:

> I need to have a compound correctly protonated to dock it. I tried to  
> use the resource of
> "upload sets" of ZINC, but it seems that it does not have the required  
> charactersitics of
> bioavailability and non-toxicity, because it gives me no output as it  
> did with other
> compounds.
> 
> The smile for this compound is:
> C1=C(C=CC2=C1C(=C[N]2)CC(=O)NCCCNCCCCNCCCNC(=O)CC3=C[N]C4=C3C=C(C=C4)Br)Br

There are a number of options:

smi23d - 3D Coordinate Generation
http://www.chembiogrid.org/cheminfo/smi23d/

Online SMILES Translator and Structure File Generator
http://cactus.nci.nih.gov/services/translate/

Molecule file conversion with MolConverter
http://www.chemaxon.com/marvin/doc/user/molconvert.html

Search the CCL for others:
http://www.ccl.net/


Once you get an xyz representation then you can apply other tools
to study and modify the protonation, such as Chimera, reduce, LEaP, etc.

Scott



From sbrozell at scripps.edu  Fri Oct 26 18:44:25 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Fri, 26 Oct 2007 18:44:25 -0700 (PDT)
Subject: [Dock-fans] Fwd: Long bonds
In-Reply-To: <32221.9540.qm@web57611.mail.re1.yahoo.com>
Message-ID: <Pine.SGI.4.51.0710231834180.81097-100000@pusar.scripps.edu>

Hi,

On Mon, 22 Oct 2007, Francesco Pietra wrote:

> Sorry, forgot: how to recognize where the protons are on histidine, so that
> HIE can be changed to HID? Similarly for aspartic.

I probably do not understand the question; did you examine the 
structures in a visualizer, such as Chimera, VMD, etc.
See the Amber score tutorial or the Amber manual for the definition
of HID, HIE, etc.
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm
See below.

> --- Francesco Pietra <chiendarret at yahoo.com> wrote:
> 
> > With my large protein and ligand I was able to carry out docking, both rigid
> > and flex ligand. Amber_score failed because of two kinds of problems with the
> > protein.

> > 1st PROBLEM (protons on histidine, etc): 
> > FATAL:  Atom .R<GLU 443>.A<HE1 16> does not have a type.
> > FATAL:  Atom .R<HIE 441>.A<HD1 18> does not have a type.
> > FATAL:  Atom .R<ASP 402>.A<HD1 13> does not have a type.
> > FATAL:  Atom .R<ASP 386>.A<HD1 13> does not have a type.

> > Is that better in such cases to edit the names by hand (problematic with
> > aspartic, H on O), or make recourse to (a) downlodable sourceforge softw, (b)
> > "biophysics" softw on server?

The appropriate method depends on several factors including your
confidence in the existing protonation versus your confidence
in those produced by tools, as well as whether the existing proton
states/coordinates need to be preserved.  See these for additional comments:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-January/000892.html
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-January/000876.html

> > ----------------------------

> > 2nd PROBLEM:

> > WARNING: There is a bond of 50.040630 angstroms between: 
> > -------  .R<THR 333>.A<C 13> and .R<SER 334>.A<N 1>
> > WARNING: There is a bond of 39.464740 angstroms between: 
> > -------  .R<THR 222>.A<C 13> and .R<SER 223>.A<N 1>
> > WARNING: There is a bond of 49.372740 angstroms between: 

> > I was advised to insert "TER" records between the residues that the bond is
> > connecting. For the first long bond, is that correct as follows:

The central issue is whether there should be a bond between these
residues ?  If not then insert TER cards after each separate
molecule.  If there should be a bond then the initial xyz coordinates
are screwed up.

Scott

...
> > ATOM   5150  OG1 THR X 333      13.670 -12.723  22.556  0.00  0.00           
> > ATOM   5151  HG1 THR X 333      12.831 -13.194  22.522  0.00  0.00           
> > ATOM   5152  C   THR X 333      14.755 -14.634  24.443  0.00  0.00           
> > ATOM   5153  O   THR X 333      15.694 -15.150  25.132  0.00  0.00 
> > TER           
> > ATOM   5154  N   SER X 334     -16.176  22.312  10.940  0.00  0.00           
> > ATOM   5155  H   SER X 334     -15.301  22.760  10.966  0.00  0.00           
> > ATOM   5156  CA  SER X 334     -16.224  20.932  11.429  0.00  0.00           
...


From chiendarret at yahoo.com  Sat Oct 27 06:33:15 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Sat, 27 Oct 2007 06:33:15 -0700 (PDT)
Subject: [Dock-fans] Fwd: Long bonds
In-Reply-To: <Pine.SGI.4.51.0710231834180.81097-100000@pusar.scripps.edu>
Message-ID: <38280.70377.qm@web57603.mail.re1.yahoo.com>


--- Scott Brozell <sbrozell at scripps.edu> wrote:

> Hi,
> 
> On Mon, 22 Oct 2007, Francesco Pietra wrote:
> 
> > Sorry, forgot: how to recognize where the protons are on histidine, so that
> > HIE can be changed to HID? Similarly for aspartic.
> 
> I probably do not understand the question; did you examine the 
> structures in a visualizer, such as Chimera, VMD, etc.
> See the Amber score tutorial or the Amber manual for the definition
> of HID, HIE, etc.
> http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm
> See below.

Thanks. Soon after posting, all that became clear using Chimera. 

As you kindly examined my problem, I feel myself obliged to tell what I also
did in the meantime.


> 
> > --- Francesco Pietra <chiendarret at yahoo.com> wrote:
> > 
> > > With my large protein and ligand I was able to carry out docking, both
> rigid
> > > and flex ligand. Amber_score failed because of two kinds of problems with
> the
> > > protein.
> 
> > > 1st PROBLEM (protons on histidine, etc): 
> > > FATAL:  Atom .R<GLU 443>.A<HE1 16> does not have a type.
> > > FATAL:  Atom .R<HIE 441>.A<HD1 18> does not have a type.
> > > FATAL:  Atom .R<ASP 402>.A<HD1 13> does not have a type.
> > > FATAL:  Atom .R<ASP 386>.A<HD1 13> does not have a type.
> 
> > > Is that better in such cases to edit the names by hand (problematic with
> > > aspartic, H on O), or make recourse to (a) downlodable sourceforge softw,
> (b)
> > > "biophysics" softw on server?
> 
> The appropriate method depends on several factors including your
> confidence in the existing protonation versus your confidence
> in those produced by tools, as well as whether the existing proton
> states/coordinates need to be preserved.  See these for additional comments:
> http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-January/000892.html
> http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-January/000876.html

See PS, please. I'll go though these suggestions.
> 
> > > ----------------------------
> 
> > > 2nd PROBLEM:
> 
> > > WARNING: There is a bond of 50.040630 angstroms between: 
> > > -------  .R<THR 333>.A<C 13> and .R<SER 334>.A<N 1>
> > > WARNING: There is a bond of 39.464740 angstroms between: 
> > > -------  .R<THR 222>.A<C 13> and .R<SER 223>.A<N 1>
> > > WARNING: There is a bond of 49.372740 angstroms between: 
> 
> > > I was advised to insert "TER" records between the residues that the bond
> is
> > > connecting. For the first long bond, is that correct as follows:
> 
> The central issue is whether there should be a bond between these
> residues ?  If not then insert TER cards after each separate
> molecule.  If there should be a bond then the initial xyz coordinates
> are screwed up.


In removing peripheral helices from the protein, perhaps because of my modest
experience, those long bonds formed from unsaturated valencies. Because they
should not be present  (they just cross the opening of the pore in its widest
"diameter", as detected with Chimera, while VMD - as I used it  default - did
not reveal them) I inserted "TER" on columns 1-3 between the relevant residues,
whereby there were no more such long bonds on loading the pdb to Chimera. That
occurred several days ago.

I did also other editing to pdb
(a) rename HIS -> HID
(b) Rename ASP and GLU -> ASH and GLH, resp. This required also exchanging the
name of the oxygens and rename the proton, which was on the "wrong" oxygen.
(c) Delete unwanted N-terminal 'H' hydrogens.

That cleaned much the protein, though not completely. Dock-Prep - through
out-of-place questions, arrived at non-integral charges. At this point I was
lost. The problem is being kindly examined by the Chimera team. I did not try
to fix with Amber 9 tleap.

Regards
francesco

PS: I also tried to use pdq2pqr. On forming the pqr file with the sole
"--ff=amber" all three "TER" were removed without compensating with hydrogens.
The file did no more open with Chimera, which found alleged non-adherence to
the pdb format. VDM opened it. The option "--with-ph=7.4" (which is just the pH
at which experiments have been carried out with the protein) the error was
"unable to find propka", although the compilation with propka was correct. I
dropped the matter because that probably is not the right way to get the pdb
following the rules.


> 
> Scott
> 
> ...
> > > ATOM   5150  OG1 THR X 333      13.670 -12.723  22.556  0.00  0.00       
>    
> > > ATOM   5151  HG1 THR X 333      12.831 -13.194  22.522  0.00  0.00       
>    
> > > ATOM   5152  C   THR X 333      14.755 -14.634  24.443  0.00  0.00       
>    
> > > ATOM   5153  O   THR X 333      15.694 -15.150  25.132  0.00  0.00 
> > > TER           
> > > ATOM   5154  N   SER X 334     -16.176  22.312  10.940  0.00  0.00       
>    
> > > ATOM   5155  H   SER X 334     -15.301  22.760  10.966  0.00  0.00       
>    
> > > ATOM   5156  CA  SER X 334     -16.224  20.932  11.429  0.00  0.00       
>    
> ...
> 
> 


__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

From sbrozell at scripps.edu  Sat Oct 27 12:22:24 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Sat, 27 Oct 2007 12:22:24 -0700 (PDT)
Subject: [Dock-fans] Fwd: Long bonds
In-Reply-To: <38280.70377.qm@web57603.mail.re1.yahoo.com>
Message-ID: <Pine.LNX.4.44.0710271149150.12022-100000@loyd.scripps.edu>

Hi,

On Sat, 27 Oct 2007, Francesco Pietra wrote:

> --- Scott Brozell <sbrozell at scripps.edu> wrote:
> 
> > On Mon, 22 Oct 2007, Francesco Pietra wrote:
> > 
> > > Sorry, forgot: how to recognize where the protons are on histidine, so that
> > > HIE can be changed to HID? Similarly for aspartic.
> > 
> > I probably do not understand the question; did you examine the 
> > structures in a visualizer, such as Chimera, VMD, etc.
> > See the Amber score tutorial or the Amber manual for the definition
> > of HID, HIE, etc.
> > http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm
> > See below.
> 
> Thanks. Soon after posting, all that became clear using Chimera. 
> 
> As you kindly examined my problem, I feel myself obliged to tell what I also
> did in the meantime.
> 
> 
> > > --- Francesco Pietra <chiendarret at yahoo.com> wrote:
> > > 
> > > > With my large protein and ligand I was able to carry out docking, both
> > rigid
> > > > and flex ligand. Amber_score failed because of two kinds of problems with
> > the
> > > > protein.
> > 
> > > > 1st PROBLEM (protons on histidine, etc): 
> > > > FATAL:  Atom .R<GLU 443>.A<HE1 16> does not have a type.
> > > > FATAL:  Atom .R<HIE 441>.A<HD1 18> does not have a type.
> > > > FATAL:  Atom .R<ASP 402>.A<HD1 13> does not have a type.
> > > > FATAL:  Atom .R<ASP 386>.A<HD1 13> does not have a type.
> > 
> > > > Is that better in such cases to edit the names by hand (problematic with
> > > > aspartic, H on O), or make recourse to (a) downlodable sourceforge softw,
> > (b)
> > > > "biophysics" softw on server?
> > 
> > The appropriate method depends on several factors including your
> > confidence in the existing protonation versus your confidence
> > in those produced by tools, as well as whether the existing proton
> > states/coordinates need to be preserved.  See these for additional comments:
> > http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-January/000892.html
> > http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-January/000876.html
> 
> See PS, please. I'll go though these suggestions.
> > 
> > > > ----------------------------
> > 
> > > > 2nd PROBLEM:
> > 
> > > > WARNING: There is a bond of 50.040630 angstroms between: 
> > > > -------  .R<THR 333>.A<C 13> and .R<SER 334>.A<N 1>
> > > > WARNING: There is a bond of 39.464740 angstroms between: 
> > > > -------  .R<THR 222>.A<C 13> and .R<SER 223>.A<N 1>
> > > > WARNING: There is a bond of 49.372740 angstroms between: 
> > 
> > > > I was advised to insert "TER" records between the residues that the bond
> > is
> > > > connecting. For the first long bond, is that correct as follows:
> > 
> > The central issue is whether there should be a bond between these
> > residues ?  If not then insert TER cards after each separate
> > molecule.  If there should be a bond then the initial xyz coordinates
> > are screwed up.
> 
> 
> In removing peripheral helices from the protein, perhaps because of my modest
> experience, those long bonds formed from unsaturated valencies. Because they
> should not be present  (they just cross the opening of the pore in its widest
> "diameter", as detected with Chimera, while VMD - as I used it  default - did
> not reveal them) I inserted "TER" on columns 1-3 between the relevant residues,
> whereby there were no more such long bonds on loading the pdb to Chimera. That
> occurred several days ago.
> 
> I did also other editing to pdb
> (a) rename HIS -> HID
> (b) Rename ASP and GLU -> ASH and GLH, resp. This required also exchanging the
> name of the oxygens and rename the proton, which was on the "wrong" oxygen.
> (c) Delete unwanted N-terminal 'H' hydrogens.
> 
> That cleaned much the protein, though not completely. Dock-Prep - through
> out-of-place questions, arrived at non-integral charges. At this point I was
> lost. The problem is being kindly examined by the Chimera team. I did not try
> to fix with Amber 9 tleap.


In most visualization programs one can select and remove pieces,
such as peripheral helices, and I would expect the result to be clean
with respect to capping dangling bonds.
Significant reworking of the starting structure is occurring.
In the big picture this may be reasonable, but getting all the details
correct may be challenging.  I recommend running some intermediate steps
through LEaP since it can be fussy.

I have not used pdb2pqr.

Scott

> PS: I also tried to use pdq2pqr. On forming the pqr file with the sole
> "--ff=amber" all three "TER" were removed without compensating with hydrogens.
> The file did no more open with Chimera, which found alleged non-adherence to
> the pdb format. VDM opened it. The option "--with-ph=7.4" (which is just the pH
> at which experiments have been carried out with the protein) the error was
> "unable to find propka", although the compilation with propka was correct. I
> dropped the matter because that probably is not the right way to get the pdb
> following the rules.
> 
> 
> > 
> > Scott
> > 
> > ...
> > > > ATOM   5150  OG1 THR X 333      13.670 -12.723  22.556  0.00  0.00       
> >    
> > > > ATOM   5151  HG1 THR X 333      12.831 -13.194  22.522  0.00  0.00       
> >    
> > > > ATOM   5152  C   THR X 333      14.755 -14.634  24.443  0.00  0.00       
> >    
> > > > ATOM   5153  O   THR X 333      15.694 -15.150  25.132  0.00  0.00 
> > > > TER           
> > > > ATOM   5154  N   SER X 334     -16.176  22.312  10.940  0.00  0.00       
> >    
> > > > ATOM   5155  H   SER X 334     -15.301  22.760  10.966  0.00  0.00       
> >    
> > > > ATOM   5156  CA  SER X 334     -16.224  20.932  11.429  0.00  0.00       
> >    
> > ...
> > 
> > 
> 
> 
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around 
> http://mail.yahoo.com 
> 

-- 



From sbrozell at scripps.edu  Sat Oct 27 12:33:57 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Sat, 27 Oct 2007 12:33:57 -0700 (PDT)
Subject: [Dock-fans] Unbiased docking
In-Reply-To: <849495.84468.qm@web57614.mail.re1.yahoo.com>
Message-ID: <Pine.LNX.4.44.0710262050310.12022-100000@loyd.scripps.edu>

Hi,

On Sun, 21 Oct 2007, Francesco Pietra wrote:

> Based on the suggestions below, I have followed the layout and settings of the
> Dock6.1-web-page tutorials for my model pore protein (3400 heavy atoms, noH, no
> solvent added) and 150-atoms neutral, lipidic ligand (bearing all hydrogens),
> using the minimum energy conformation of the latter from Amber9 simulated
> annealing in vacuum.
> 
> sphgen failed, while sphgen_cpp built re.ms and rec.sph in a few minutes,
> 118807 surface points in 91 clusters. I was surprised to see roughly the same
> sphere distribution for clusters # 1, 2, and 91. Hope that sounds correct. I
> did not examine other clusters, and all was done very roughly at the open eye.
> 
> Grid OK in ca 1h and half.
> 
> Rigid docking completed in 5 min wall time, showing the elongated ligand (made
> of annealed rings) inside the cone, with the head out. Grid score -52.3.
> 
> Flex docking (cpu time ca 3h; anchors 1; orientations 500, conformations 115,
> grid score -69.2, vdw -67.2, es -2). The arrangement of the ligand within the
> pore was roughly the same as for rigid  docking, through the head of the ligand
> was docked differently.
> 
> I did not carry out any docking with higher-energy conformers of the ligand.


I do not notice any red flags in the above, but I do not have any
experience with pore proteins.

> This long story because it is the first time I am at docking outside tutorials,
> to hopefully get suggestions as to go on. I could either carry out amber score,
> and the relevant tutorial I have found outside the dock web page is clear
> enough. Is that what Scott had in mind when he kindly suggested "go to Amber
> after docking, and with the MD results back to Dock" or should I rather skip
> amber scoring and go directly to Amber 9 to carry out a regular MD, may be with
> the pore model inside POPC? If so, which is the shortest way to use my above
> results from DOCK to set up the Amber 9 MD? (I mean, how to save the pore
> protein plus the ligand so that Amber 9 can work; I am familiar with prmtop and
> inprc file, while I read that Amber 9 can't import mol2 files with more than
> one residue; if I save protein+ligand as pdb, how to get parameters for the
> ligand? Or, if I save the protein and ligand separately do they conserve their
> respective positions?.


My recollection is that I suggested DOCK for docking and Amber for MD.
There are a number of ways to go from docking results to MD.
If you rescore with Amber Score in DOCK then the Amber score preparation
and the DOCK outputs contain Amber readable prmtop and inpcrd files.
See
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
for a description of the output files.  Also running DOCK with the
verbose flag, -v, may help to see what's happening under the hood.
(Currently the verbose output follows the normal DOCK output
when -o is used; so first try -v without -o.)

Scott

> --- Scott Brozell <sbrozell at scripps.edu> wrote:
> 
> > Hi,
> > 
> > On Fri, 28 Sep 2007, Francesco Pietra wrote:
> > 
> > > Although not yet ready with DOCK6.1 installation, inspection of tutorials
> > > prompts a couple of questions that may help planning.
> > >
> > > What I want to do at the moment is verifying if there is docking at all
> > between
> > > a family of natural products and a complicated protein. Not in a bilayer
> > for
> > > the moment.
> > >
> > > I have already carried out a conformational search for my natural products
> > by
> > > simulated annealing with an algorithm that calls Amber9. Parameter and
> > > coordinate files for Amber9 were built with Antechamber/Divcon (ie AM1).
> > >
> > > The tutorial on DOCK web site starts from a protein-ligand complex, ie from
> > a
> > > definite receptor site in the protein. Is any graphical or alphanumeric
> > > tutorial for the unbiased docking I am aimed at?
> > 
> > Not that I am aware of.
> > There is a lot of flexibility in binding sites selection;
> > see step 3 of
> >
> http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm
> > If your complicated protein is big then that may put a practical limit
> > on the size of your grid; one approach would be to divide and conquer
> > the big protein binding sites into subsets that would be processed
> > separately.
> > Perhaps others have comments ?
> > 
> > > DOCK6.1 is being compiled on a parallel amd64 machine (Debian Linux amd64
> > with
> > > 4GB RAM per cpu, ie a machine better suited for ab initio calculations than
> > > classical MD), where also Amber9 is installed. Although the X system exists
> > (in
> > > fact, xleap requires it) and even Gnome could be called, the machine is
> > > normally used with X killed. I manage anything graphical for Amber9 (to the
> > > exception of xleap) on a single-Athlon desktop (Debian Linux i386 etch).
> > The
> > > two machines are scp linked, which is the way I exchange files between the
> > two
> > > machines.
> > >
> > > At 32bit I (1) prepare pdb files for "small molecules" with a MM package;
> > (2)
> > > examine everything graphical with VMD.
> > >
> > > On these basis, where to install Chimera for DOCK? I noticed that Chimera
> > calls
> > > both Dock Prep and Antechamber.
> > 
> > 
> > Installing Chimera on the same machine as VMD seems reasonable.
> > Any textual input and output files can be communicated between the machines.
> > 
> > > Similarly, where to install dms for DOCK?
> > 
> > dms is small.  I install it in my dock directory.
> > 
> > 
> > > I understand that these are generic question, normally not for mailing
> > lists.
> > > Though, a couple of suggestions would greatly help me (an organic chemist,
> > just
> > > now beginning to touch the area of the biochemist) in the high complexity
> > of
> > > the docking affairs.
> > 
> > 
> > This is the best place for all questions.
> > 
> > Scott




From sbrozell at scripps.edu  Sat Oct 27 12:51:24 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Sat, 27 Oct 2007 12:51:24 -0700 (PDT)
Subject: [Dock-fans] Calcium  problem with amber score
In-Reply-To: <575569.63737.qm@web43131.mail.sp1.yahoo.com>
Message-ID: <Pine.LNX.4.44.0710271238380.12022-100000@loyd.scripps.edu>

Hi,

> On Thu, 18 Oct 2007, Osmany Guirola wrote:
> 
> I am trying to use the amber score but i am having problems with
> the prepare_amberize.pl script...my pdb file has a Ca ion and this is the error in the log file
> 
> For atom: .R<CA 45>.A<CA 1> Could not find type: Ca
> Parameter file was not saved.
>         Quit
> 
> of course my rec*.prmtop files have 0kb size
> what can i do?

Read these:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-February/000896.html
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-May/001024.html
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-September/000723.html

Note that searching the dock fans archives at 
http://dock.compbio.ucsf.edu/DOCK_6/index.htm
is currently missing some posts due to technical issues that
we are trying to fix.

Scott



From chiendarret at yahoo.com  Sat Oct 27 13:23:10 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Sat, 27 Oct 2007 13:23:10 -0700 (PDT)
Subject: [Dock-fans] Unbiased docking
In-Reply-To: <Pine.LNX.4.44.0710262050310.12022-100000@loyd.scripps.edu>
Message-ID: <449821.17481.qm@web57613.mail.re1.yahoo.com>


--- Scott Brozell <sbrozell at scripps.edu> wrote:

> Hi,
> 
> On Sun, 21 Oct 2007, Francesco Pietra wrote:
> 
> > Based on the suggestions below, I have followed the layout and settings of
> the
> > Dock6.1-web-page tutorials for my model pore protein (3400 heavy atoms,
> noH, no
> > solvent added) and 150-atoms neutral, lipidic ligand (bearing all
> hydrogens),
> > using the minimum energy conformation of the latter from Amber9 simulated
> > annealing in vacuum.
> > 
> > sphgen failed, while sphgen_cpp built re.ms and rec.sph in a few minutes,
> > 118807 surface points in 91 clusters. I was surprised to see roughly the
> same
> > sphere distribution for clusters # 1, 2, and 91. Hope that sounds correct.
> I
> > did not examine other clusters, and all was done very roughly at the open
> eye.
> > 
> > Grid OK in ca 1h and half.
> > 
> > Rigid docking completed in 5 min wall time, showing the elongated ligand
> (made
> > of annealed rings) inside the cone, with the head out. Grid score -52.3.
> > 
> > Flex docking (cpu time ca 3h; anchors 1; orientations 500, conformations
> 115,
> > grid score -69.2, vdw -67.2, es -2). The arrangement of the ligand within
> the
> > pore was roughly the same as for rigid  docking, through the head of the
> ligand
> > was docked differently.
> > 
> > I did not carry out any docking with higher-energy conformers of the
> ligand.
> 
> 
> I do not notice any red flags in the above, but I do not have any
> experience with pore proteins.

As I told in the thread on "TER removed", red flags came with amber_score in
DOCK6.1. While the files associated with the ligand were OK, the inpcrd and
prmtop files were desolatingly empty. The error log suggested some of the steps
about which I told on the "TER removed" thread. Coming the first time at
docking, and with a pore protein model, which was also my first creation of
pores, I didn't expect any rapid success. It will be an exciting experience if
I finally succeed. I am most curios if the docking I observed is specific of
that molecule (I know experimentally that it interacts with the pore protein).
Once Amber simulations will also succeed, I'll try with other molecules of that
family which do not affect the pore protein. Then, should the lipid bilayer be
present? The ligands are strictly lipidic.

Thanks
francesco


> 
> > This long story because it is the first time I am at docking outside
> tutorials,
> > to hopefully get suggestions as to go on. I could either carry out amber
> score,
> > and the relevant tutorial I have found outside the dock web page is clear
> > enough. Is that what Scott had in mind when he kindly suggested "go to
> Amber
> > after docking, and with the MD results back to Dock" or should I rather
> skip
> > amber scoring and go directly to Amber 9 to carry out a regular MD, may be
> with
> > the pore model inside POPC? If so, which is the shortest way to use my
> above
> > results from DOCK to set up the Amber 9 MD? (I mean, how to save the pore
> > protein plus the ligand so that Amber 9 can work; I am familiar with prmtop
> and
> > inprc file, while I read that Amber 9 can't import mol2 files with more
> than
> > one residue; if I save protein+ligand as pdb, how to get parameters for the
> > ligand? Or, if I save the protein and ligand separately do they conserve
> their
> > respective positions?.
> 
> 
> My recollection is that I suggested DOCK for docking and Amber for MD.
> There are a number of ways to go from docking results to MD.
> If you rescore with Amber Score in DOCK then the Amber score preparation
> and the DOCK outputs contain Amber readable prmtop and inpcrd files.
> See
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
> for a description of the output files.  Also running DOCK with the
> verbose flag, -v, may help to see what's happening under the hood.
> (Currently the verbose output follows the normal DOCK output
> when -o is used; so first try -v without -o.)
> 
> Scott
> 
> > --- Scott Brozell <sbrozell at scripps.edu> wrote:
> > 
> > > Hi,
> > > 
> > > On Fri, 28 Sep 2007, Francesco Pietra wrote:
> > > 
> > > > Although not yet ready with DOCK6.1 installation, inspection of
> tutorials
> > > > prompts a couple of questions that may help planning.
> > > >
> > > > What I want to do at the moment is verifying if there is docking at all
> > > between
> > > > a family of natural products and a complicated protein. Not in a
> bilayer
> > > for
> > > > the moment.
> > > >
> > > > I have already carried out a conformational search for my natural
> products
> > > by
> > > > simulated annealing with an algorithm that calls Amber9. Parameter and
> > > > coordinate files for Amber9 were built with Antechamber/Divcon (ie
> AM1).
> > > >
> > > > The tutorial on DOCK web site starts from a protein-ligand complex, ie
> from
> > > a
> > > > definite receptor site in the protein. Is any graphical or alphanumeric
> > > > tutorial for the unbiased docking I am aimed at?
> > > 
> > > Not that I am aware of.
> > > There is a lot of flexibility in binding sites selection;
> > > see step 3 of
> > >
> >
>
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm
> > > If your complicated protein is big then that may put a practical limit
> > > on the size of your grid; one approach would be to divide and conquer
> > > the big protein binding sites into subsets that would be processed
> > > separately.
> > > Perhaps others have comments ?
> > > 
> > > > DOCK6.1 is being compiled on a parallel amd64 machine (Debian Linux
> amd64
> > > with
> > > > 4GB RAM per cpu, ie a machine better suited for ab initio calculations
> than
> > > > classical MD), where also Amber9 is installed. Although the X system
> exists
> > > (in
> > > > fact, xleap requires it) and even Gnome could be called, the machine is
> > > > normally used with X killed. I manage anything graphical for Amber9 (to
> the
> > > > exception of xleap) on a single-Athlon desktop (Debian Linux i386
> etch).
> > > The
> > > > two machines are scp linked, which is the way I exchange files between
> the
> > > two
> > > > machines.
> > > >
> > > > At 32bit I (1) prepare pdb files for "small molecules" with a MM
> package;
> > > (2)
> > > > examine everything graphical with VMD.
> > > >
> > > > On these basis, where to install Chimera for DOCK? I noticed that
> Chimera
> > > calls
> > > > both Dock Prep and Antechamber.
> > > 
> > > 
> > > Installing Chimera on the same machine as VMD seems reasonable.
> > > Any textual input and output files can be communicated between the
> machines.
> > > 
> > > > Similarly, where to install dms for DOCK?
> > > 
> > > dms is small.  I install it in my dock directory.
> > > 
> > > 
> > > > I understand that these are generic question, normally not for mailing
> > > lists.
> > > > Though, a couple of suggestions would greatly help me (an organic
> chemist,
> > > just
> > > > now beginning to touch the area of the biochemist) in the high
> complexity
> > > of
> > > > the docking affairs.
> > > 
> > > 
> > > This is the best place for all questions.
> > > 
> > > Scott
> 
> 
> 
> 


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From sbrozell at scripps.edu  Sun Oct 28 11:31:49 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Sun, 28 Oct 2007 10:31:49 -0800 (PST)
Subject: [Dock-fans] Unbiased docking
In-Reply-To: <449821.17481.qm@web57613.mail.re1.yahoo.com>
Message-ID: <Pine.LNX.4.44.0710281024550.12022-100000@loyd.scripps.edu>

Hi,

On Sat, 27 Oct 2007, Francesco Pietra wrote:

> --- Scott Brozell <sbrozell at scripps.edu> wrote:
> 
> > On Sun, 21 Oct 2007, Francesco Pietra wrote:
> > 
> > > Based on the suggestions below, I have followed the layout and settings of
> > the
> > > Dock6.1-web-page tutorials for my model pore protein (3400 heavy atoms,
> > noH, no
> > > solvent added) and 150-atoms neutral, lipidic ligand (bearing all
> > hydrogens),
> > > using the minimum energy conformation of the latter from Amber9 simulated
> > > annealing in vacuum.
> > > 
> > > sphgen failed, while sphgen_cpp built re.ms and rec.sph in a few minutes,
> > > 118807 surface points in 91 clusters. I was surprised to see roughly the
> > same
> > > sphere distribution for clusters # 1, 2, and 91. Hope that sounds correct.
> > I
> > > did not examine other clusters, and all was done very roughly at the open
> > eye.
> > > 
> > > Grid OK in ca 1h and half.
> > > 
> > > Rigid docking completed in 5 min wall time, showing the elongated ligand
> > (made
> > > of annealed rings) inside the cone, with the head out. Grid score -52.3.
> > > 
> > > Flex docking (cpu time ca 3h; anchors 1; orientations 500, conformations
> > 115,
> > > grid score -69.2, vdw -67.2, es -2). The arrangement of the ligand within
> > the
> > > pore was roughly the same as for rigid  docking, through the head of the
> > ligand
> > > was docked differently.
> > > 
> > > I did not carry out any docking with higher-energy conformers of the
> > ligand.
> > 
> > 
> > I do not notice any red flags in the above, but I do not have any
> > experience with pore proteins.
> 
> As I told in the thread on "TER removed", red flags came with amber_score in
> DOCK6.1. While the files associated with the ligand were OK, the inpcrd and
> prmtop files were desolatingly empty. The error log suggested some of the steps
> about which I told on the "TER removed" thread. Coming the first time at
> docking, and with a pore protein model, which was also my first creation of
> pores, I didn't expect any rapid success. It will be an exciting experience if
> I finally succeed. I am most curios if the docking I observed is specific of
> that molecule (I know experimentally that it interacts with the pore protein).
> Once Amber simulations will also succeed, I'll try with other molecules of that
> family which do not affect the pore protein. Then, should the lipid bilayer be
> present? The ligands are strictly lipidic.


I do not have any experience simulating lipid bilayers.
Some obvious points are
how close to the lipid bilayer are the active site(s) ?
how does the lipid bilayer affect the pore protein conformation ?
is the pore protein stable (in MD) without the lipid bilayer ?

Scott

> > > This long story because it is the first time I am at docking outside
> > tutorials,
> > > to hopefully get suggestions as to go on. I could either carry out amber
> > score,
> > > and the relevant tutorial I have found outside the dock web page is clear
> > > enough. Is that what Scott had in mind when he kindly suggested "go to
> > Amber
> > > after docking, and with the MD results back to Dock" or should I rather
> > skip
> > > amber scoring and go directly to Amber 9 to carry out a regular MD, may be
> > with
> > > the pore model inside POPC? If so, which is the shortest way to use my
> > above
> > > results from DOCK to set up the Amber 9 MD? (I mean, how to save the pore
> > > protein plus the ligand so that Amber 9 can work; I am familiar with prmtop
> > and
> > > inprc file, while I read that Amber 9 can't import mol2 files with more
> > than
> > > one residue; if I save protein+ligand as pdb, how to get parameters for the
> > > ligand? Or, if I save the protein and ligand separately do they conserve
> > their
> > > respective positions?.
> > 
> > 
> > My recollection is that I suggested DOCK for docking and Amber for MD.
> > There are a number of ways to go from docking results to MD.
> > If you rescore with Amber Score in DOCK then the Amber score preparation
> > and the DOCK outputs contain Amber readable prmtop and inpcrd files.
> > See
> > http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
> > for a description of the output files.  Also running DOCK with the
> > verbose flag, -v, may help to see what's happening under the hood.
> > (Currently the verbose output follows the normal DOCK output
> > when -o is used; so first try -v without -o.)
> > 
> > Scott
> > 
> > > --- Scott Brozell <sbrozell at scripps.edu> wrote:
> > > 
> > > > Hi,
> > > > 
> > > > On Fri, 28 Sep 2007, Francesco Pietra wrote:
> > > > 
> > > > > Although not yet ready with DOCK6.1 installation, inspection of
> > tutorials
> > > > > prompts a couple of questions that may help planning.
> > > > >
> > > > > What I want to do at the moment is verifying if there is docking at all
> > > > between
> > > > > a family of natural products and a complicated protein. Not in a
> > bilayer
> > > > for
> > > > > the moment.
> > > > >
> > > > > I have already carried out a conformational search for my natural
> > products
> > > > by
> > > > > simulated annealing with an algorithm that calls Amber9. Parameter and
> > > > > coordinate files for Amber9 were built with Antechamber/Divcon (ie
> > AM1).
> > > > >
> > > > > The tutorial on DOCK web site starts from a protein-ligand complex, ie
> > from
> > > > a
> > > > > definite receptor site in the protein. Is any graphical or alphanumeric
> > > > > tutorial for the unbiased docking I am aimed at?
> > > > 
> > > > Not that I am aware of.
> > > > There is a lot of flexibility in binding sites selection;
> > > > see step 3 of
> > > >
> > >
> >
> http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm
> > > > If your complicated protein is big then that may put a practical limit
> > > > on the size of your grid; one approach would be to divide and conquer
> > > > the big protein binding sites into subsets that would be processed
> > > > separately.
> > > > Perhaps others have comments ?
> > > > 
> > > > > DOCK6.1 is being compiled on a parallel amd64 machine (Debian Linux
> > amd64
> > > > with
> > > > > 4GB RAM per cpu, ie a machine better suited for ab initio calculations
> > than
> > > > > classical MD), where also Amber9 is installed. Although the X system
> > exists
> > > > (in
> > > > > fact, xleap requires it) and even Gnome could be called, the machine is
> > > > > normally used with X killed. I manage anything graphical for Amber9 (to
> > the
> > > > > exception of xleap) on a single-Athlon desktop (Debian Linux i386
> > etch).
> > > > The
> > > > > two machines are scp linked, which is the way I exchange files between
> > the
> > > > two
> > > > > machines.
> > > > >
> > > > > At 32bit I (1) prepare pdb files for "small molecules" with a MM
> > package;
> > > > (2)
> > > > > examine everything graphical with VMD.
> > > > >
> > > > > On these basis, where to install Chimera for DOCK? I noticed that
> > Chimera
> > > > calls
> > > > > both Dock Prep and Antechamber.
> > > > 
> > > > 
> > > > Installing Chimera on the same machine as VMD seems reasonable.
> > > > Any textual input and output files can be communicated between the
> > machines.
> > > > 
> > > > > Similarly, where to install dms for DOCK?
> > > > 
> > > > dms is small.  I install it in my dock directory.
> > > > 
> > > > 
> > > > > I understand that these are generic question, normally not for mailing
> > > > lists.
> > > > > Though, a couple of suggestions would greatly help me (an organic
> > chemist,
> > > > just
> > > > > now beginning to touch the area of the biochemist) in the high
> > complexity
> > > > of
> > > > > the docking affairs.
> > > > 
> > > > 
> > > > This is the best place for all questions.
> > > > 
> > > > Scott
> > 
> > 
> > 
> > 
> 
> 
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around 
> http://mail.yahoo.com 
> 

-- 


From sbrozell at scripps.edu  Sun Oct 28 23:04:16 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Sun, 28 Oct 2007 22:04:16 -0800 (PST)
Subject: [Dock-fans] Fwd: generatin Sphere failure
In-Reply-To: <269133.36725.qm@web57614.mail.re1.yahoo.com>
Message-ID: <Pine.LNX.4.44.0710282138220.12022-100000@loyd.scripps.edu>

Hi,

On Fri, 19 Oct 2007, Francesco Pietra wrote:

> I solved the problem with Andrew Magis' sphgen_cpp 

Good.  Since you later indicated that there were
118807 surface points in 91 clusters,
it is likely that the five digit restriction on the number of spheres
caused the error when reading the intermediate file temp2.

The incorrect (9999) restriction on the number of spheres in
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm
has been corrected and will be posted soon.

Scott

> --- Francesco Pietra <chiendarret at yahoo.com> wrote:
> 
> > Date: Thu, 18 Oct 2007 09:38:37 -0700 (PDT)
> > From: Francesco Pietra <chiendarret at yahoo.com>
> > Subject: generating Sphere failure
> > To: dock-fans <dock-fans at docking.org>
> > 
> > I carried out successfully all DOCK6.1 tutorials. In contrast, when I tried
> > to
> > apply the defaults of the tutorials to a large protein (an ion channel
> > teepee),
> > I met failure at the Generating Spheres stage.
> > 
> > Command "sphgen" generated an empty teepee_noH.sph  file (the requested file
> > in
> > INSPH), alongside temp1.ms temp2.sph temp3.atc files. The error is
> > illustrated
> > in OUTSPH:
> > 
> > density type = X
> >  reading  teepee_noH.ms                                                      
> >  
> >          type   R
> >  # of atoms =   3412   # of surf pts =  *****
> >  finding spheres for   teepee_noH.ms                                         
> >  
> >                    
> >  dotlim =     0.000
> >  radmax =    4.000
> >  Minimum radius of acceptable spheres?
> >   1.39999998
> >  output to  teepee_noH.sph                                                   
> >  
> >         
> >  error reading temp2.sph
> >     0   89  1.4954  100457    0.011160   25.497364   11.149721  -10.546585
> > 
> > 
> > There are no "# of surf pts" and "temp2.sph" could not be read. Was that due
> > to
> > a too large protein or to unsuited defaults of the tutorial? Also, are the
> > temp.* files intermediate files during the computation? (they were not
> > present
> > at completed tutorial). I can't imagine if this is sufficient information for
> > a
> > rough diagnosis. It is the first time I move outside the tutorials with DOCK.


From sbrozell at scripps.edu  Sun Oct 28 23:35:32 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Sun, 28 Oct 2007 22:35:32 -0800 (PST)
Subject: [Dock-fans] when dock6.mpi crashes....
In-Reply-To: <D7E48CEB-915B-4568-8B55-42E4EDB7E408@colorado.edu>
Message-ID: <Pine.LNX.4.44.0710261904190.12022-100000@loyd.scripps.edu>

Hi,

On Wed, 3 Oct 2007, Francis E Reyes wrote:

> How about writing conformers for all molecules that were ranked?
> 
> Are those now lost?

Yes, previously ranked conformers are lost.

If one has a large library or an unstable computing environment
then one should consider printing out individual conformations
on the fly.  See
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFileOutput
Once all the calculations have completed then concatenate the output
files and run a follow up calculation that merely ranks the poses
without redocking or rescoring them.

Scott

> On Oct 3, 2007, at 9:31 AM, Scott Brozell wrote:
> 
> > On Tue, 2 Oct 2007, Francis E Reyes wrote:
> >
> >> What steps can I do to restart where it left off? I understand I
> >> could use skip_molecule, but how about ranking, writing out  
> >> conformers?
> >
> > There is no restart facility yet; see these for past comments:
> > http://shoichetlab.compbio.ucsf.edu/pipermail/dock-fans/2007-August/ 
> > 001164.html
> > http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-October/ 
> > 000750.html
> >
> > Scott




From chiendarret at yahoo.com  Mon Oct 29 03:25:11 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Mon, 29 Oct 2007 03:25:11 -0700 (PDT)
Subject: [Dock-fans] Combining DOCK with AMBER
Message-ID: <133639.35249.qm@web57610.mail.re1.yahoo.com>

I posted previously that, with DOCK6.1, dock-prep for my protein, after
repeated fixing, arrived at fractional charges for the residues. Either some
were still misnamed, or some were lacking. This was the best I could do.

Accepting the suggestion to go to Amber (someone was even skeptical that the
fractional charges for this large receptor could be assigned by Antechamber), I
have now loaded the pdb to leap (Amber9), whereby heavy atoms were added (where
I had set TER records) and H/lone pairs also added. Both prmtop and inpcrd
could be saved (and opened correctly with VMD). Of perhaps major concern
(leap.log attached):

(Residues lacking connect 0/ connect 1 -
These don't have chain types marked:
res  total affected
CTHR 4
NSER 4

Should all that be OK, how to go to DOCK now? I have prmtop and inpcrd files
also for the ligand, obtained from prepare_amber.pl, though, obviously, no such
files for the complex receptor-ligand.

Also, the receptor has 24.000000 charge: should docking be carried out with
this charged receptor or should it be first neutralized (in leap?).

I realize that this a combination of tricky problems and my limited experience.
Thanks for your understanding.

francesco pietra

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From sbrozell at scripps.edu  Mon Oct 29 13:14:43 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Mon, 29 Oct 2007 12:14:43 -0800 (PST)
Subject: [Dock-fans] Combining DOCK with AMBER
In-Reply-To: <133639.35249.qm@web57610.mail.re1.yahoo.com>
Message-ID: <Pine.LNX.4.44.0710291127140.12022-100000@loyd.scripps.edu>

Hi,

On Mon, 29 Oct 2007, Francesco Pietra wrote:

> I posted previously that, with DOCK6.1, dock-prep for my protein, after
> repeated fixing, arrived at fractional charges for the residues. Either some
> were still misnamed, or some were lacking. This was the best I could do.
> 
> Accepting the suggestion to go to Amber (someone was even skeptical that the
> fractional charges for this large receptor could be assigned by Antechamber), I
> have now loaded the pdb to leap (Amber9), whereby heavy atoms were added (where
> I had set TER records) and H/lone pairs also added. Both prmtop and inpcrd
> could be saved (and opened correctly with VMD). Of perhaps major concern
> (leap.log attached):
> 
> (Residues lacking connect 0/ connect 1 -
> These don't have chain types marked:
> res  total affected
> CTHR 4
> NSER 4

These are innocuous.  They indicate that some residues are not connected.
And those should correspond to your insertion of TER cards.  See
http://amber.ch.ic.ac.uk/archive/200502/0264.html
http://amber.ch.ic.ac.uk/archive/200505/0290.html

> Should all that be OK, how to go to DOCK now? I have prmtop and inpcrd files
> also for the ligand, obtained from prepare_amber.pl, though, obviously, no such
> files for the complex receptor-ligand.

If prepare_amber.pl was run, there should be all the Amber files (prmtop, etc)
for all three (ligand, receptor, complex).
See step 3 in
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm
Once amberization is complete and verified then use step 4 of that tutorial
as a template for creating your own dock input file for rescoring.

> Also, the receptor has 24.000000 charge: should docking be carried out with
> this charged receptor or should it be first neutralized (in leap?).

DOCK's Amber score uses an implicit solvent model in which case
charge neutralization with explicit ions is usually not performed.

Scott

> I realize that this a combination of tricky problems and my limited experience.
> Thanks for your understanding.



From chiendarret at yahoo.com  Mon Oct 29 16:48:52 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Mon, 29 Oct 2007 16:48:52 -0700 (PDT)
Subject: [Dock-fans] Combining DOCK with AMBER
In-Reply-To: <Pine.LNX.4.44.0710291127140.12022-100000@loyd.scripps.edu>
Message-ID: <199144.31269.qm@web57614.mail.re1.yahoo.com>


--- Scott Brozell <sbrozell at scripps.edu> wrote:

> Hi,
> 
> On Mon, 29 Oct 2007, Francesco Pietra wrote:
> 
> > I posted previously that, with DOCK6.1, dock-prep for my protein, after
> > repeated fixing, arrived at fractional charges for the residues. Either
> some
> > were still misnamed, or some were lacking. This was the best I could do.
> > 
> > Accepting the suggestion to go to Amber (someone was even skeptical that
> the
> > fractional charges for this large receptor could be assigned by
> Antechamber), I
> > have now loaded the pdb to leap (Amber9), whereby heavy atoms were added
> (where
> > I had set TER records) and H/lone pairs also added. Both prmtop and inpcrd
> > could be saved (and opened correctly with VMD). Of perhaps major concern
> > (leap.log attached):
> > 
> > (Residues lacking connect 0/ connect 1 -
> > These don't have chain types marked:
> > res  total affected
> > CTHR 4
> > NSER 4
> 
> These are innocuous.  They indicate that some residues are not connected.
> And those should correspond to your insertion of TER cards.  See
> http://amber.ch.ic.ac.uk/archive/200502/0264.html
> http://amber.ch.ic.ac.uk/archive/200505/0290.html

In fact, prepare_amber.pl lig.mol2 rec.pdb produced the expected files, though

mpirun -np 4 dock6.mpi -i dock.in -o dock.out

after the "Initialing MPI Routines for all nodes, said

"getpdb: can't open file 0.amber.pdb"

The dock.out.# don't tell much.

This rec.pdb failed with Dock-prep in Chimera. Again, the program believes that
there are non-standard residue, assigning them to Antechamber, which produces
fractional charges for the residues.

In other words, I did not succeed in getting Chimera and DOCK talking 
together.

Thanks

francesco

 
> 
> > Should all that be OK, how to go to DOCK now? I have prmtop and inpcrd
> files
> > also for the ligand, obtained from prepare_amber.pl, though, obviously, no
> such
> > files for the complex receptor-ligand.
> 
> If prepare_amber.pl was run, there should be all the Amber files (prmtop,
> etc)
> for all three (ligand, receptor, complex).
> See step 3 in
> http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm
> Once amberization is complete and verified then use step 4 of that tutorial
> as a template for creating your own dock input file for rescoring.
> 
> > Also, the receptor has 24.000000 charge: should docking be carried out with
> > this charged receptor or should it be first neutralized (in leap?).
> 
> DOCK's Amber score uses an implicit solvent model in which case
> charge neutralization with explicit ions is usually not performed.
> 
> Scott
> 
> > I realize that this a combination of tricky problems and my limited
> experience.
> > Thanks for your understanding.
> 
> 
> 


__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
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From sbrozell at scripps.edu  Mon Oct 29 19:32:59 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Mon, 29 Oct 2007 18:32:59 -0800 (PST)
Subject: [Dock-fans] Combining DOCK with AMBER
In-Reply-To: <199144.31269.qm@web57614.mail.re1.yahoo.com>
Message-ID: <Pine.LNX.4.44.0710291818110.12022-100000@loyd.scripps.edu>

Hi,

On Mon, 29 Oct 2007, Francesco Pietra wrote:

> --- Scott Brozell <sbrozell at scripps.edu> wrote:
> 
> > On Mon, 29 Oct 2007, Francesco Pietra wrote:
> > 
> > > I posted previously that, with DOCK6.1, dock-prep for my protein, after
> > > repeated fixing, arrived at fractional charges for the residues. Either
> > some
> > > were still misnamed, or some were lacking. This was the best I could do.
> > > 
> > > Accepting the suggestion to go to Amber (someone was even skeptical that
> > the
> > > fractional charges for this large receptor could be assigned by
> > Antechamber), I
> > > have now loaded the pdb to leap (Amber9), whereby heavy atoms were added
> > (where
> > > I had set TER records) and H/lone pairs also added. Both prmtop and inpcrd
> > > could be saved (and opened correctly with VMD). Of perhaps major concern
> > > (leap.log attached):
> > > 
> > > (Residues lacking connect 0/ connect 1 -
> > > These don't have chain types marked:
> > > res  total affected
> > > CTHR 4
> > > NSER 4
> > 
> > These are innocuous.  They indicate that some residues are not connected.
> > And those should correspond to your insertion of TER cards.  See
> > http://amber.ch.ic.ac.uk/archive/200502/0264.html
> > http://amber.ch.ic.ac.uk/archive/200505/0290.html
> 
> In fact, prepare_amber.pl lig.mol2 rec.pdb produced the expected files, though
> 
> mpirun -np 4 dock6.mpi -i dock.in -o dock.out
> 
> after the "Initialing MPI Routines for all nodes, said
> 
> "getpdb: can't open file 0.amber.pdb"
> 
> The dock.out.# don't tell much.


http://dock.compbio.ucsf.edu/DOCK_6/6.1/bugfix.2

> This rec.pdb failed with Dock-prep in Chimera. Again, the program believes that
> there are non-standard residue, assigning them to Antechamber, which produces
> fractional charges for the residues.
> 
> In other words, I did not succeed in getting Chimera and DOCK talking 
> together.


I probably do not understand exactly what you are doing,
why run Dock-prep again ?
Perhaps you should open the amberized receptor files in Chimera:
rec.amber.pdb
rec.prmtop
etc

Scott

> > > Should all that be OK, how to go to DOCK now? I have prmtop and inpcrd
> > files
> > > also for the ligand, obtained from prepare_amber.pl, though, obviously, no
> > such
> > > files for the complex receptor-ligand.
> > 
> > If prepare_amber.pl was run, there should be all the Amber files (prmtop,
> > etc)
> > for all three (ligand, receptor, complex).
> > See step 3 in
> > http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm
> > Once amberization is complete and verified then use step 4 of that tutorial
> > as a template for creating your own dock input file for rescoring.
> > 
> > > Also, the receptor has 24.000000 charge: should docking be carried out with
> > > this charged receptor or should it be first neutralized (in leap?).
> > 
> > DOCK's Amber score uses an implicit solvent model in which case
> > charge neutralization with explicit ions is usually not performed.
> > 
> > Scott
> > 
> > > I realize that this a combination of tricky problems and my limited
> > experience.
> > > Thanks for your understanding.


From chiendarret at yahoo.com  Tue Oct 30 02:55:32 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Tue, 30 Oct 2007 02:55:32 -0700 (PDT)
Subject: [Dock-fans] Combining DOCK with AMBER
In-Reply-To: <Pine.LNX.4.44.0710291818110.12022-100000@loyd.scripps.edu>
Message-ID: <350486.31681.qm@web57607.mail.re1.yahoo.com>


--- Scott Brozell <sbrozell at scripps.edu> wrote:

> Hi,
> 
> On Mon, 29 Oct 2007, Francesco Pietra wrote:
> 
> > --- Scott Brozell <sbrozell at scripps.edu> wrote:
> > 
> > > On Mon, 29 Oct 2007, Francesco Pietra wrote:
> > > 
> > > > I posted previously that, with DOCK6.1, dock-prep for my protein, after
> > > > repeated fixing, arrived at fractional charges for the residues. Either
> > > some
> > > > were still misnamed, or some were lacking. This was the best I could
> do.
> > > > 
> > > > Accepting the suggestion to go to Amber (someone was even skeptical
> that
> > > the
> > > > fractional charges for this large receptor could be assigned by
> > > Antechamber), I
> > > > have now loaded the pdb to leap (Amber9), whereby heavy atoms were
> added
> > > (where
> > > > I had set TER records) and H/lone pairs also added. Both prmtop and
> inpcrd
> > > > could be saved (and opened correctly with VMD). Of perhaps major
> concern
> > > > (leap.log attached):
> > > > 
> > > > (Residues lacking connect 0/ connect 1 -
> > > > These don't have chain types marked:
> > > > res  total affected
> > > > CTHR 4
> > > > NSER 4
> > > 
> > > These are innocuous.  They indicate that some residues are not connected.
> > > And those should correspond to your insertion of TER cards.  See
> > > http://amber.ch.ic.ac.uk/archive/200502/0264.html
> > > http://amber.ch.ic.ac.uk/archive/200505/0290.html
> > 
> > In fact, prepare_amber.pl lig.mol2 rec.pdb produced the expected files,
> though
> > 
> > mpirun -np 4 dock6.mpi -i dock.in -o dock.out
> > 
> > after the "Initialing MPI Routines for all nodes, said
> > 
> > "getpdb: can't open file 0.amber.pdb"
> > 
> > The dock.out.# don't tell much.
> 
> 
> http://dock.compbio.ucsf.edu/DOCK_6/6.1/bugfix.2

Ah! I failed to look at dock-fans. Sorry. However, the edited file (attached
base_mpi.cpp) gives the same error (getpdb: can't open file 0.amber.pdb) as the
original file (attached original_base_mpi.cpp).

Probably I was unable to follow the recipe, and there is no one around here
capable of C or C++. I simply deleted a line of program from the original file.

I have checked that the prmtop and inpcrd files generated by prepare_amber.pl
produce the correct representation in both VMD and Chimera.


> 
> > This rec.pdb failed with Dock-prep in Chimera. Again, the program believes
> that
> > there are non-standard residue, assigning them to Antechamber, which
> produces
> > fractional charges for the residues.
> > 
> > In other words, I did not succeed in getting Chimera and DOCK talking 
> > together.
> 
> 
> I probably do not understand exactly what you are doing,
> why run Dock-prep again ?

It was to check if the pdb fixed by LEAP was now OK for DockPrep. It was not.

Thanks
francesco

> Perhaps you should open the amberized receptor files in Chimera:
> rec.amber.pdb
> rec.prmtop
> etc
> 
> Scott
> 
> > > > Should all that be OK, how to go to DOCK now? I have prmtop and inpcrd
> > > files
> > > > also for the ligand, obtained from prepare_amber.pl, though, obviously,
> no
> > > such
> > > > files for the complex receptor-ligand.
> > > 
> > > If prepare_amber.pl was run, there should be all the Amber files (prmtop,
> > > etc)
> > > for all three (ligand, receptor, complex).
> > > See step 3 in
> > > http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm
> > > Once amberization is complete and verified then use step 4 of that
> tutorial
> > > as a template for creating your own dock input file for rescoring.
> > > 
> > > > Also, the receptor has 24.000000 charge: should docking be carried out
> with
> > > > this charged receptor or should it be first neutralized (in leap?).
> > > 
> > > DOCK's Amber score uses an implicit solvent model in which case
> > > charge neutralization with explicit ions is usually not performed.
> > > 
> > > Scott
> > > 
> > > > I realize that this a combination of tricky problems and my limited
> > > experience.
> > > > Thanks for your understanding.
> 
> 


__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 
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From sbrozell at scripps.edu  Tue Oct 30 18:03:00 2007
From: sbrozell at scripps.edu (Scott Brozell)
Date: Tue, 30 Oct 2007 17:03:00 -0800 (PST)
Subject: [Dock-fans] Combining DOCK with AMBER
In-Reply-To: <350486.31681.qm@web57607.mail.re1.yahoo.com>
Message-ID: <Pine.LNX.4.44.0710301658200.20140-100000@loyd.scripps.edu>

Hi,

On Tue, 30 Oct 2007, Francesco Pietra wrote:

> --- Scott Brozell <sbrozell at scripps.edu> wrote:
> 
> > On Mon, 29 Oct 2007, Francesco Pietra wrote:
> > 
> > > --- Scott Brozell <sbrozell at scripps.edu> wrote:
> > > 
> > > > On Mon, 29 Oct 2007, Francesco Pietra wrote:
> > > > 
> > > > > I posted previously that, with DOCK6.1, dock-prep for my protein, after
> > > > > repeated fixing, arrived at fractional charges for the residues. Either
> > > > some
> > > > > were still misnamed, or some were lacking. This was the best I could
> > do.
> > > > > 
> > > > > Accepting the suggestion to go to Amber (someone was even skeptical
> > that
> > > > the
> > > > > fractional charges for this large receptor could be assigned by
> > > > Antechamber), I
> > > > > have now loaded the pdb to leap (Amber9), whereby heavy atoms were
> > added
> > > > (where
> > > > > I had set TER records) and H/lone pairs also added. Both prmtop and
> > inpcrd
> > > > > could be saved (and opened correctly with VMD). Of perhaps major
> > concern
> > > > > (leap.log attached):
> > > > > 
> > > > > (Residues lacking connect 0/ connect 1 -
> > > > > These don't have chain types marked:
> > > > > res  total affected
> > > > > CTHR 4
> > > > > NSER 4
> > > > 
> > > > These are innocuous.  They indicate that some residues are not connected.
> > > > And those should correspond to your insertion of TER cards.  See
> > > > http://amber.ch.ic.ac.uk/archive/200502/0264.html
> > > > http://amber.ch.ic.ac.uk/archive/200505/0290.html
> > > 
> > > In fact, prepare_amber.pl lig.mol2 rec.pdb produced the expected files,
> > though
> > > 
> > > mpirun -np 4 dock6.mpi -i dock.in -o dock.out
> > > 
> > > after the "Initialing MPI Routines for all nodes, said
> > > 
> > > "getpdb: can't open file 0.amber.pdb"
> > > 
> > > The dock.out.# don't tell much.
> > 
> > 
> > http://dock.compbio.ucsf.edu/DOCK_6/6.1/bugfix.2
> 
> Ah! I failed to look at dock-fans. Sorry. However, the edited file (attached
> base_mpi.cpp) gives the same error (getpdb: can't open file 0.amber.pdb) as the
> original file (attached original_base_mpi.cpp).
> 
> Probably I was unable to follow the recipe, and there is no one around here
> capable of C or C++. I simply deleted a line of program from the original file.
> 
> I have checked that the prmtop and inpcrd files generated by prepare_amber.pl
> produce the correct representation in both VMD and Chimera.


base_mpi.cpp has been correctly patched.  Reinstall dock:
cd install; make dock

Scott

> > > This rec.pdb failed with Dock-prep in Chimera. Again, the program believes
> > that
> > > there are non-standard residue, assigning them to Antechamber, which
> > produces
> > > fractional charges for the residues.
> > > 
> > > In other words, I did not succeed in getting Chimera and DOCK talking 
> > > together.
> > 
> > 
> > I probably do not understand exactly what you are doing,
> > why run Dock-prep again ?
> 
> It was to check if the pdb fixed by LEAP was now OK for DockPrep. It was not.
> 
> Thanks
> francesco
> 
> > Perhaps you should open the amberized receptor files in Chimera:
> > rec.amber.pdb
> > rec.prmtop
> > etc
> > 
> > Scott
> > 
> > > > > Should all that be OK, how to go to DOCK now? I have prmtop and inpcrd
> > > > files
> > > > > also for the ligand, obtained from prepare_amber.pl, though, obviously,
> > no
> > > > such
> > > > > files for the complex receptor-ligand.
> > > > 
> > > > If prepare_amber.pl was run, there should be all the Amber files (prmtop,
> > > > etc)
> > > > fo