From ksvinaykumar at gmail.com  Sat Dec  1 21:25:56 2007
From: ksvinaykumar at gmail.com (Vinay Kumar)
Date: Sun, 2 Dec 2007 10:55:56 +0530
Subject: [Dock-fans] ligand -regding
Message-ID: <ef4e9c1a0712012125s32ef8a47p689486a4bc5acc04@mail.gmail.com>

Hello dockers,

I would like to know,
1) why is it that only polar hydrogens are added in the macromolecule?
2) if we need to add all hydrogens (polar and non-polar) explicitly to
the ligand while a docking is performed? for ex- if the ligand is
phenol, do i have to draw the phenyl ring with CH2 explicitly shown,
or just use the ring structure provided by the drawing interface?

would like your thoughts,

regards,
Vinay

From jji at cgl.ucsf.edu  Sat Dec  1 21:46:08 2007
From: jji at cgl.ucsf.edu (John J. Irwin)
Date: Sat, 01 Dec 2007 21:46:08 -0800
Subject: [Dock-fans] ligand -regding
In-Reply-To: <ef4e9c1a0712012125s32ef8a47p689486a4bc5acc04@mail.gmail.com>
References: <ef4e9c1a0712012125s32ef8a47p689486a4bc5acc04@mail.gmail.com>
Message-ID: <475246A0.5000907@cgl.ucsf.edu>

Hi Vinay

It would be helpful for you to tell us a bit more about what program(s)
and options you are using. Which version of docking software? Which
drawing interface?

In general, if you are using a united-atom scoring function, then you
only want polar hydrogens on the protein. If you are using an all atom
scoring function, then you will need all H atoms to be explicit. You
always need (at least for all versions of DOCK) a ligand with all atoms
explicitly represented, for example as found in ZINC.

Good luck

John
johnirwin.docking.org


Vinay Kumar wrote:
> Hello dockers,
>
> I would like to know,
> 1) why is it that only polar hydrogens are added in the macromolecule?
> 2) if we need to add all hydrogens (polar and non-polar) explicitly to
> the ligand while a docking is performed? for ex- if the ligand is
> phenol, do i have to draw the phenyl ring with CH2 explicitly shown,
> or just use the ring structure provided by the drawing interface?
>
> would like your thoughts,
>
> regards,
> Vinay
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>   

From ksvinaykumar at gmail.com  Sun Dec  2 00:43:33 2007
From: ksvinaykumar at gmail.com (Vinay Kumar)
Date: Sun, 2 Dec 2007 14:13:33 +0530
Subject: [Dock-fans] ligand -regding
In-Reply-To: <475246A0.5000907@cgl.ucsf.edu>
References: <ef4e9c1a0712012125s32ef8a47p689486a4bc5acc04@mail.gmail.com>
	<475246A0.5000907@cgl.ucsf.edu>
Message-ID: <ef4e9c1a0712020043r37e962e0j843dd99b1a012bc5@mail.gmail.com>

Hi again,
I use MDL ISIS draw (free) software for drawing my ligands, save it,
and port it through Babel, which would give me, mol2 or pdb output
files, which i can use as input ligand file in DOCK. i hope this is
what was asked for!! (and please tell me, if my method mentioned above
is ok?)

is there anyway, i can know, what scoring function is in use, and can
i change it in DOCK?

With regards,
Vinay


On Dec 2, 2007 11:16 AM, John J. Irwin <jji at cgl.ucsf.edu> wrote:
> Hi Vinay
>
> It would be helpful for you to tell us a bit more about what program(s)
> and options you are using. Which version of docking software? Which
> drawing interface?
>
> In general, if you are using a united-atom scoring function, then you
> only want polar hydrogens on the protein. If you are using an all atom
> scoring function, then you will need all H atoms to be explicit. You
> always need (at least for all versions of DOCK) a ligand with all atoms
> explicitly represented, for example as found in ZINC.
>
> Good luck
>
> John
> johnirwin.docking.org
>
>
>
> Vinay Kumar wrote:
> > Hello dockers,
> >
> > I would like to know,
> > 1) why is it that only polar hydrogens are added in the macromolecule?
> > 2) if we need to add all hydrogens (polar and non-polar) explicitly to
> > the ligand while a docking is performed? for ex- if the ligand is
> > phenol, do i have to draw the phenyl ring with CH2 explicitly shown,
> > or just use the ring structure provided by the drawing interface?
> >
> > would like your thoughts,
> >
> > regards,
> > Vinay
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >
>

From devleena at scripps.edu  Mon Dec  3 11:16:21 2007
From: devleena at scripps.edu (Devleena)
Date: Mon, 3 Dec 2007 11:16:21 -0800 (PST)
Subject: [Dock-fans] amber score in dock 6.1 (Yubo Fan)
In-Reply-To: <mailman.45269.1196574375.4213.dock-fans@docking.org>
Message-ID: <Pine.SGI.3.96.1071203111117.250650A-100000@gamow>

Hi Yubo,

You need to use the nab_atom_expression for that purpose.
Check AMBERScore section in DOCK 6 manual:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
For ex, if your ligand is strand 2 and protein is strand 1, the
nab_atom_expression for ligand and residue 20-30 flexible would
be: 2::|1:20,21,22,23,24,25,26,27,29,30

Hope this helps.

Devleena

> ------------------------------
> 
> Message: 5
> Date: Thu, 29 Nov 2007 13:38:17 -0600
> From: "Yubo Fan" <yubofan at mail.chem.tamu.edu>
> Subject: [Dock-fans] amber score in dock 6.1
> To: <dock-fans at docking.org>,	<CHEMISTRY at ccl.net>
> Message-ID: <001001c832bf$63efee70$94b25ba5 at yubopcatlab>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hello,
> 
> I have a question about setting the flexible region for docking with UCSF Dock 6.1.
> 
> If I need to set the ligand and certain amino acid residues as movable
> region, how can I define them. For example, how can I set the ligand and
> residue 20-30 movable for docking in the keyword shown below? 
> amber_score_movable_region [ligand] (distance, everything, ligand,
> nab_atom_expression, nothing): 
> 
> Thanks a lot,
> 
> Yubo
> ============================================================
> Yubo Fan  Ph.D             Email: yubofan at mail.chem.tamu.edu
> Department of Chemistry    Tel:   1-979-845-5237
> Texas A&M University
> College Station, TX 77843
> ============================================================


From szhong at rx.umaryland.edu  Tue Dec  4 09:53:06 2007
From: szhong at rx.umaryland.edu (Zhong, Shijun)
Date: Tue, 4 Dec 2007 12:53:06 -0500
Subject: [Dock-fans] Using Dock for "blind-docking" (Ben Keshet)
References: <mailman.45269.1196574375.4213.dock-fans@docking.org>
Message-ID: <99ACB209EDC58343B189A58BBA1B55FA04580062@cits-exch1.campus.umaryland.edu>

Hi Ben,

We did use DOCK to identify binding site. Please see the paper:
Zhong, S.; MacKerell, A. D., Jr.
Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces
J. Chem. Inf. Model; (Article); 2007; 47(6); 2303-2315.
Hope it will be helpful for solving your problem.


Shijun Zhong


-----Original Message-----


Today's Topics:

   1. Using Dock for "blind-docking" (Ben Keshet)


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

Message: 1
Date: Wed, 21 Nov 2007 10:37:42 -0500
From: "Ben Keshet" <keshet1 at umbc.edu>
Subject: [Dock-fans] Using Dock for "blind-docking"
To: <dock-fans at docking.org>
Message-ID: <200711211537.lALFbm9m026604 at smtp.umbc.edu>
Content-Type: text/plain;	charset="us-ascii"

I have followed recently the discussion here regarding the capabilities of
docking, when the binding site is unknown. It was written by a Dock-team
member (John Irwin) that:

"...We start with docking once we know the binding site. Are you asking if
docking can be used to rank binding sites by the likelihood that one binds a
particular ligand? Sure, why not, give it a try. But given the famously high
false positive rate of docking, the odds are against you".

I have a somewhat similar problem to Francesco's and would appreciate your
opinion.  

There is little information available about the binding site of my receptor,
but there are several attractive alternatives.  I am using Dock to bind
several inhibitors separately to each possible binding site, while I am
gradually increasing the radius of spheres to be included at each binding
site. 

For example, I (1) use "select_spheres" to select the spheres at 5A from the
possible site, (2) use Dock to predict the binding, and (3) expand the
spheres in the binding site to 8A, and repeat the docking (and increasing
radius and so on).  I stop when increasing the radius of spheres included
does not significantly change the binding pose.  

At the end I have ~5 possible binding configurations.  I then use
Amber_score to refine them and allow better judgment of the poses.
Eventually, I hope to be able to utilize this information to experimentally
test these binding sites (mutagenesis, modifications).   

Even though I think that this is not the original usage method that Dock was
designed for, does that seem as a reasonable approach or do you still
believe that the "odds are against me"? 

As Dock being my docking tool, I would greatly appreciate any thoughts and
comments you might have.

On another note - it says on your website that tutorials for "Rescoring DOCK
Runs with Solvation Scoring Functions" and "DOCK 3.5 Scoring Functions" will
be coming soon.  Do you have any estimation on when it will be available?  

Thanks you,
Ben Keshet




From lujing1999 at 126.com  Wed Dec  5 23:10:41 2007
From: lujing1999 at 126.com (=?gb2312?Q?=C2=B9=BE=A7jinger.Lu?=)
Date: Thu, 6 Dec 2007 15:10:41 +0800 (CST)
Subject: [Dock-fans] error happened when I ran felxiable  dock ing
Message-ID: <4757A071.00001A.30950@bj126app9.126.com>

Hi, dock-fans, 
 I am trying to dock  a set of ligands using flexible ligand docking. I used the file  tutorial /mpi_demo/4_dock/mpi.in as the template .  Using sphere_slector, I selected the sphere within 6.0Ang of the ligand. with the generated .sph file , I created a box using showbox with extra margin of 5A. After running dock6.mpi , the job gave the following output :
Molecule: Palmitoyl glycine
 Elapsed time:  2 seconds
 ERROR:  Could not complete growth. 
         Confirm grid box is large enough to contain 
         ligand and try increasing max_orients.
there are 60 molecule in my set, and 41  are showed errors like that.  I also ran serial dock with the same parameter file, and the same 41 ligands showed same errors. I also tried a single molecule , and got the same error message. Otherwise, I tried rigid docking also using the same ligands set, and no errors showed.  
the following is the output file when I tried a single molecule . please let me know if I am missing something here. thanks for your help
 
--------------------------------------
DOCK v6.1
Released December 2006
Copyright UCSF
--------------------------------------

Molecule Library Input Parameters
------------------------------------------------------------------------------------------
ligand_atom_file                                             test.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
Orient Ligand Parameters
------------------------------------------------------------------------------------------
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           ../2_site/rec.sph
max_orientations                                             500
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
Flexible Ligand Parameters
------------------------------------------------------------------------------------------
flexible_ligand                                              yes
min_anchor_size                                              40
pruning_use_clustering                                       yes
pruning_max_orients                                          100
pruning_clustering_cutoff                                    100
use_internal_energy                                          yes
internal_energy_att_exp                                      6
internal_energy_rep_exp                                      12
internal_energy_dielectric                                   4.0
use_clash_overlap                                            no
Bump Filter Parameters
------------------------------------------------------------------------------------------
bump_filter                                                  no
Master Score Parameters
------------------------------------------------------------------------------------------
score_molecules                                              yes
Contact Score Paramters
------------------------------------------------------------------------------------------
contact_score_primary                                        no
contact_score_secondary                                      no
Grid Score Parameters
------------------------------------------------------------------------------------------
grid_score_primary                                           yes
grid_score_secondary                                         no
grid_score_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       ../3_grid/grid
Dock3.5 Score Parameters
------------------------------------------------------------------------------------------
dock3.5_score_secondary                                      no
Continuous Energy Score Parameters
------------------------------------------------------------------------------------------
continuous_score_secondary                                   no
Zou GB/SA Score Parameters
------------------------------------------------------------------------------------------
gbsa_zou_score_secondary                                     no
Hawkins GB/SA Score Parameters
------------------------------------------------------------------------------------------
gbsa_hawkins_score_secondary                                 no
Amber Score Parameters
------------------------------------------------------------------------------------------
amber_score_secondary                                        no
Warning:  No secondary scoring function selected.

Simplex Minimization Parameters
------------------------------------------------------------------------------------------
minimize_ligand                                              yes
minimize_anchor                                              yes
minimize_flexible_growth                                     yes
use_advanced_simplex_parameters                              no
simplex_max_cycles                                           1
simplex_score_converge                                       0.1
simplex_cycle_converge                                       1.0
simplex_trans_step                                           1.0
simplex_rot_step                                             0.1
simplex_tors_step                                            10.0
simplex_anchor_max_iterations                                500
simplex_grow_max_iterations                                  500
simplex_final_min                                            no
simplex_random_seed                                          0
Atom Typing Parameters
------------------------------------------------------------------------------------------
atom_model                                                   all
vdw_defn_file                                                ../../parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               ../../parameters/flex.defn
flex_drive_file                                              ../../parameters/flex_drive.tbl
Molecule Library Output Parameters
------------------------------------------------------------------------------------------
ligand_outfile_prefix                                        1G3J_2801
write_orientations                                           no
num_scored_conformers_written                                1
rank_ligands                                                 no
------------------------------------------------------------------------------------------
Initializing Library File Routines...
Initializing Orienting Routines...
Initializing Conformer Generator Routines...
Initializing Grid Score Routines...
 Reading the energy grid from ../3_grid/grid.nrg
-----------------------------------
Molecule: Docosahexaenoyl ethanolamide
 Elapsed time:  3 seconds
 ERROR:  Could not complete growth. 
         Confirm grid box is large enough to contain 
         ligand and try increasing max_orients.


 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20071206/74ad7240/attachment-0001.html 

From jji at cgl.ucsf.edu  Thu Dec  6 12:02:09 2007
From: jji at cgl.ucsf.edu (John J. Irwin)
Date: Thu, 06 Dec 2007 12:02:09 -0800
Subject: [Dock-fans] ligand -regding
In-Reply-To: <ef4e9c1a0712020043r37e962e0j843dd99b1a012bc5@mail.gmail.com>
References: <ef4e9c1a0712012125s32ef8a47p689486a4bc5acc04@mail.gmail.com>	
	<475246A0.5000907@cgl.ucsf.edu>
	<ef4e9c1a0712020043r37e962e0j843dd99b1a012bc5@mail.gmail.com>
Message-ID: <47585541.2070902@cgl.ucsf.edu>

Hi Vinay

Since you are using ISIS Draw -> (Open?) Babel, Babel should look after
adding all protons. You need to pay attention to the protonation,
charge, and tautomeric form (if relevant) of your molecule created in
this way.

All versions of DOCK support several scoring functions, and rather than
repeat what is in the manual, I'll just refer you here to the manual and
the literature for guidance about which one is most appropriate for your
target.

Hope this helps

John


Vinay Kumar wrote:
> Hi again,
> I use MDL ISIS draw (free) software for drawing my ligands, save it,
> and port it through Babel, which would give me, mol2 or pdb output
> files, which i can use as input ligand file in DOCK. i hope this is
> what was asked for!! (and please tell me, if my method mentioned above
> is ok?)
>
> is there anyway, i can know, what scoring function is in use, and can
> i change it in DOCK?
>
> With regards,
> Vinay
>
>
> On Dec 2, 2007 11:16 AM, John J. Irwin <jji at cgl.ucsf.edu> wrote:
>   
>> Hi Vinay
>>
>> It would be helpful for you to tell us a bit more about what program(s)
>> and options you are using. Which version of docking software? Which
>> drawing interface?
>>
>> In general, if you are using a united-atom scoring function, then you
>> only want polar hydrogens on the protein. If you are using an all atom
>> scoring function, then you will need all H atoms to be explicit. You
>> always need (at least for all versions of DOCK) a ligand with all atoms
>> explicitly represented, for example as found in ZINC.
>>
>> Good luck
>>
>> John
>> johnirwin.docking.org
>>
>>
>>
>> Vinay Kumar wrote:
>>     
>>> Hello dockers,
>>>
>>> I would like to know,
>>> 1) why is it that only polar hydrogens are added in the macromolecule?
>>> 2) if we need to add all hydrogens (polar and non-polar) explicitly to
>>> the ligand while a docking is performed? for ex- if the ligand is
>>> phenol, do i have to draw the phenyl ring with CH2 explicitly shown,
>>> or just use the ring structure provided by the drawing interface?
>>>
>>> would like your thoughts,
>>>
>>> regards,
>>> Vinay
>>> _______________________________________________
>>> Dock-fans mailing list
>>> Dock-fans at docking.org
>>> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>>>
>>>       

From jji at cgl.ucsf.edu  Thu Dec  6 14:42:03 2007
From: jji at cgl.ucsf.edu (John J. Irwin)
Date: Thu, 06 Dec 2007 14:42:03 -0800
Subject: [Dock-fans] Using Dock for "blind-docking"
In-Reply-To: <200711211537.lALFbm9m026604@smtp.umbc.edu>
References: <200711211537.lALFbm9m026604@smtp.umbc.edu>
Message-ID: <47587ABB.20301@cgl.ucsf.edu>

Hi Ben

Thank you for your email. Sorry to take so long to get back to you.

I think is an interesting application of DOCK, and merits further study
as to whether it can be used as a general protocol. To convince a
skeptical reviewer, you would want to show that this worked on, say, 40
targets, retrospectively, and that you had not just cherry picked your
examples (i.e. only report results that work). Ideally, you would also
like to use it prospectively on at least a few targets, and show that
you were able to make a prediction that was confirmed by experiment, at
least some of the time.
>  
>
> On another note - it says on your website that tutorials for "Rescoring DOCK
> Runs with Solvation Scoring Functions" and "DOCK 3.5 Scoring Functions" will
> be coming soon.  Do you have any estimation on when it will be available?  
>   
I'm not working on it ! ;-) I think the "get version 3.5.54 features
fully into version 6" work is on hold at the moment, awaiting a new
postdoc to work on it. Thus I don't think there is a timeline, but
perhaps someone who reads this will know better.

John

From lujing1999 at 126.com  Thu Dec 13 01:18:52 2007
From: lujing1999 at 126.com (=?gb2312?Q?=C2=B9=BE=A7jinger.Lu?=)
Date: Thu, 13 Dec 2007 17:18:52 +0800 (CST)
Subject: [Dock-fans] how to fix a  "could not complet growth"  error
Message-ID: <4760F8FC.00013F.30746@bj126app8.126.com>

Hi, dock fans, I ran flexiable docking with dock6.1 and have ran into a problem below :
ERROR:  Could not complete growth. 
        Confirm grid box is large enough to contain 
        ligand and try increasing max_orients.

 
I read messages from :http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-August/000694.html , which said turning off the bump checking to fix the problem , but the problem is that I used "bump_filter   no" in my parameter file,  the following is the parameters I used . Is there something  wrong?
 
--------------------------------------
DOCK v6.1
Released December 2006
Copyright UCSF
--------------------------------------

Molecule Library Input Parameters
------------------------------------------------------------------------------------------
ligand_atom_file                                             dru.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
Orient Ligand Parameters
------------------------------------------------------------------------------------------
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           ../2_site/rec.sph
max_orientations                                             5000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
Flexible Ligand Parameters
------------------------------------------------------------------------------------------

flexible_ligand                                              yes
min_anchor_size                                              15
pruning_use_clustering                                       yes
pruning_max_orients                                          100
pruning_clustering_cutoff                                    100
use_internal_energy                                          yes
internal_energy_att_exp                                      6
internal_energy_rep_exp                                      12
internal_energy_dielectric                                   4.0
use_clash_overlap                                            no
Bump Filter Parameters
------------------------------------------------------------------------------------------
bump_filter                                                  no
Master Score Parameters
------------------------------------------------------------------------------------------
score_molecules                                              yes
Contact Score Paramters
------------------------------------------------------------------------------------------
contact_score_primary                                        no
contact_score_secondary                                      no
Grid Score Parameters
------------------------------------------------------------------------------------------
grid_score_primary                                           yes
grid_score_secondary                                         no
grid_score_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       ../3_grid/grid
Dock3.5 Score Parameters
------------------------------------------------------------------------------------------
dock3.5_score_secondary                                      no
Continuous Energy Score Parameters
------------------------------------------------------------------------------------------
continuous_score_secondary                                   no
Zou GB/SA Score Parameters
------------------------------------------------------------------------------------------
gbsa_zou_score_secondary                                     no
Hawkins GB/SA Score Parameters
------------------------------------------------------------------------------------------
gbsa_hawkins_score_secondary                                 no
Amber Score Parameters
------------------------------------------------------------------------------------------
amber_score_secondary                                        no
Warning:  No secondary scoring function selected.

Simplex Minimization Parameters
------------------------------------------------------------------------------------------
minimize_ligand                                              yes
minimize_anchor                                              yes
minimize_flexible_growth                                     yes
use_advanced_simplex_parameters                              no
simplex_max_cycles                                           1
simplex_score_converge                                       0.1
simplex_cycle_converge                                       1.0
simplex_trans_step                                           1.0
simplex_rot_step                                             0.1
simplex_tors_step                                            10.0
simplex_anchor_max_iterations                                500
simplex_grow_max_iterations                                  500
simplex_final_min                                            no
simplex_random_seed                                          0
Atom Typing Parameters
------------------------------------------------------------------------------------------
atom_model                                                   all
vdw_defn_file                                                ../../parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               ../../parameters/flex.defn
flex_drive_file                                              ../../parameters/flex_drive.tbl
Molecule Library Output Parameters
------------------------------------------------------------------------------------------
ligand_outfile_prefix                                        druggable
write_orientations                                           no
num_scored_conformers_written                                1
rank_ligands                                                 no
------------------------------------------------------------------------------------------
Initializing Library File Routines...
Initializing Orienting Routines...
Initializing Conformer Generator Routines...
Initializing Grid Score Routines...
 Reading the energy grid from ../3_grid/grid.nrg
-----------------------------------
Molecule: AST 4892090
 Elapsed time:  40 seconds
 ERROR:  Could not complete growth. 
         Confirm grid box is large enough to contain 
         ligand and try increasing max_orients.

1 Molecules Processed


-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20071213/48780fb2/attachment-0001.html 

From christopher.hattan at gmail.com  Thu Dec 13 19:37:51 2007
From: christopher.hattan at gmail.com (Christopher Hattan)
Date: Thu, 13 Dec 2007 21:37:51 -0600
Subject: [Dock-fans] Compile
Message-ID: <4761FA8F.1000104@gmail.com>

How do you begin compiling DOCK for MACs


From keshet1 at umbc.edu  Fri Dec 14 14:41:43 2007
From: keshet1 at umbc.edu (Ben Keshet)
Date: Fri, 14 Dec 2007 17:41:43 -0500
Subject: [Dock-fans] Running the Test Tuite with Cygwin
In-Reply-To: <mailman.50641.1197537546.4213.dock-fans@docking.org>
Message-ID: <200712142241.lBEMfhJN001699@smtp.umbc.edu>


I am using Dock6.1 with cygwin on my PC. I tried to run the test set
available online but ran into a problem when running the scripts.  

Generally, when I am using the commands in cygsin, I need to add "./" before
the executable file (e.g. ./dock6 -i dock.in -o dock. out, or ./showbox,
etc.).

The whole test set is in my dock6/bin directory such that it is in the same
directory with all dock6 executable files. 

However, the script is unable to execute showbox and grid: 
1A28
showbox: Command not found
grid: Command not found

I tried to edit the script and added "./" before showbox, but I am getting
the same error.  

Does anyone have any suggestions? 

Thank you,

Ben 



From jji at cgl.ucsf.edu  Fri Dec 14 15:19:11 2007
From: jji at cgl.ucsf.edu (John J. Irwin)
Date: Fri, 14 Dec 2007 15:19:11 -0800
Subject: [Dock-fans] Running the Test Tuite with Cygwin
In-Reply-To: <200712142241.lBEMfhJN001699@smtp.umbc.edu>
References: <200712142241.lBEMfhJN001699@smtp.umbc.edu>
Message-ID: <47630F6F.4080600@cgl.ucsf.edu>

$ export PATH=${HOME}/dock6/bin:.:${PATH}
$ which showbox
/home/jji/dock6/bin/showbox

Good luck


Ben Keshet wrote:
> I am using Dock6.1 with cygwin on my PC. I tried to run the test set
> available online but ran into a problem when running the scripts.  
>
> Generally, when I am using the commands in cygsin, I need to add "./" before
> the executable file (e.g. ./dock6 -i dock.in -o dock. out, or ./showbox,
> etc.).
>
> The whole test set is in my dock6/bin directory such that it is in the same
> directory with all dock6 executable files. 
>
> However, the script is unable to execute showbox and grid: 
> 1A28
> showbox: Command not found
> grid: Command not found
>
> I tried to edit the script and added "./" before showbox, but I am getting
> the same error.  
>
> Does anyone have any suggestions? 
>
> Thank you,
>
> Ben 
>
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>   

From chiendarret at yahoo.com  Mon Dec 17 09:45:24 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Mon, 17 Dec 2007 09:45:24 -0800 (PST)
Subject: [Dock-fans] Fwd: Re:  Fwd: Large ligand on Large grid Kill mpirun
Message-ID: <290034.98704.qm@web57606.mail.re1.yahoo.com>

A bad printing mistake below. I meant "cluster analysis* when I wrote
"average". I know that averaging would bring things far from what I need to
compare.
Sorry
francesco

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

> Date: Mon, 17 Dec 2007 00:11:12 -0800 (PST)
> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: Re: [Dock-fans] Fwd: Large ligand on Large grid Kill mpirun
> To: Scott Brozell <sbrozell at scripps.edu>
> 
> Hi Scott:
> This is not to remind the problem below of super-large ligands. Rather, it is
> to tell that I have much advanced with Amber9 in treating the best scored
> protein-ligand (= complex) from DOCK6.1 amber-score (for a 118-atoms ligand).
> 
> The complex was placed in a 80x80A hydrated POPC membrane and treated along
> the
> lines of Amber tutorial A3. Everything went on smoothly. Now I have the first
> production run (500 ps).
> 
> Before continuing with productions runs, my question is how to compare DOCK
> amber-score docking with Amber MD. Grossly, MD has grossly maintained the
> ligand is in the same area of the pore, while examination of a couple of MD
> snapshots shows differences in detail. I mean that, within 2.6A distance from
> the ligand, the protein residues are different in amber-scoring vs Amber-MD.
> 
> With Chimera I have also carried out a rmsd analysis of the production run
> but
> I guess that for the comparison of Amber MD with DOCK I should carry out
> "average" with ptraj. 
> 
> If that is correct, it would only provide guesses on closeness between
> protein
> residues and ligand. What I would really to calculate are binding free
> energies
> for ligand in the complex vs free (both immersed in the membrane) but I find
> no
> way. A post on Amber did not provide help. Aqvist in Uppsala carries out the
> analysis of binding free energies with his "linear interaction energy"
> method,
> which works in a explicit environment. Apparently, there is no similar
> software
> in Amber, where MM_PBSA, if I understand, makes recourse to GB, which is not
> what I would like to do.
> 
> Thanks for your comments
> 
> francesco
> 
> 
> --- Scott Brozell <sbrozell at scripps.edu> wrote:
> 
> > Hi Francesco,
> > 
> > There may be some opportunities to reduce the memory use of
> > Orient::match_ligand.  However,  I'll be out of contact for
> > about two weeks.
> > 
> > Scott
> > 
> > On Sun, 18 Nov 2007, Francesco Pietra wrote:
> > 
> > > There are 4GB ram (in 2GB slots Kingston ecc 400MHz) per processor (for a
> > total
> > > of 16GB ram) and Linux is set to let all that be used. Perhaps you may
> > suggest
> > > how to set the configuration better in order that all ram is used by
> DOCK.
> > >
> > > With the slightly smaller ligands, where DOCK run correctly, I detected
> > through
> > > "top -i" a max of 24% memory used by one of the two processors in use.
> All
> > four
> > > processors were only used during amber rescore, and only for the initial
> > half
> > > reriod of the procedure. Then, the number dropped to two even for amber
> > > rescore.
> > > Thanks
> > > francesco
> > >
> > > --- Scott Brozell <sbrozell at scripps.edu> wrote:
> > >
> > > > Hi,
> > > >
> > > > The failure occurs in Orient::match_ligand.
> > > > This is the focal point of much memory consumption.
> > > > The simplest patch would be additional hardware memory.
> > > >
> > > > Scott
> > > >
> > > > On Fri, 16 Nov 2007, Francesco Pietra wrote:
> > > >
> > > > > I forgot an important observation: docking procedures went on
> regularly
> > > > even
> > > > > for the largest (155 and 165 atoms) ligands when, on previous runs,
> the
> > > > spheres
> > > > > covered ca 1/4 of the protein.
> > > > >
> > > > > --- Francesco Pietra <chiendarret at yahoo.com> wrote:
> > > > >
> > > > > > Date: Fri, 16 Nov 2007 02:11:22 -0800 (PST)
> > > > > > From: Francesco Pietra <chiendarret at yahoo.com>
> > > > > > Subject: Large ligand on Large grid Kill mpirun
> > > > > > To: dock-fans <dock-fans at docking.org>
> > > > > >
> > > > > > Following careful comparative runs I arrived at the conclusion that
> > too
> > > > large
> > > > > > ligands on large grids kill mpirun.
> > > > > >
> > > > > > With grid files and selected_spheres.sph (10,536,750 grid points),
> > for
> > > > > > ligands
> > > > > > of 118 atoms, or less, docking and amber rescore procedures went to
> > > > > > completion
> > > > > > OK. Selected spheres was centered (Magis' sphere_select)
> > symmetrically in
> > > > the
> > > > > > protein for a 25A radius, whereby the spheres covered most of the
> > > > protein.
> > > > > >
> > > > > > mpirun failure occurred with two ligands of much similar shape as
> > above
> > > > > > though
> > > > > > larger (155 atoms and 165 atoms)
> > > > > >
> > > > > >
> > > > > > How mpirun was killed shortly after launching the rigid score
> > procedure,
> > > > is
> > > > > > shown by outputting the screen events following "mpirun -np 4 -i
> > rigid.in
> > > > -o
> > > > > > rigid.out 2>&1 | tee screen.out":
> > > > > >
> > > > > > Initializing MPI Routines...
> > > > > > Initializing MPI Routines...
> > > > > > Initializing MPI Routines...
> > > > > > Initializing MPI Routines...
> > > > > > terminate called after throwing an instance of 'std::bad_alloc'
> > > > > >   what():  St9bad_alloc
> > > > > > [deb64:03725] *** Process received signal ***
> > > > > > [deb64:03725] Signal: Aborted (6)
> > > > > > [deb64:03725] Signal code:  (-6)
> > > > > > [deb64:03725] [ 0] /lib/libpthread.so.0 [0x2b21e08e0410]
> > > > > > [deb64:03725] [ 1] /lib/libc.so.6(gsignal+0x3b) [0x2b21e0a1807b]
> > > > > > [deb64:03725] [ 2] /lib/libc.so.6(abort+0x10e) [0x2b21e0a1984e]
> > > > > > [deb64:03725] [ 3]
> > > > > >
> > > >
> > /usr/lib/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x114)
> > > > > > [0x2b21e0583424]
> > > > > > [deb64:03725] [ 4] /usr/lib/libstdc++.so.6 [0x2b21e05815a6]
> > > > > > [deb64:03725] [ 5] /usr/lib/libstdc++.so.6 [0x2b21e05815d3]
> > > > > > [deb64:03725] [ 6] /usr/lib/libstdc++.so.6 [0x2b21e05816ba]
> > > > > > [deb64:03725] [ 7] dock6.mpi(main+0) [0x42c180]
> > > > > > [deb64:03725] [ 8] /usr/lib/libstdc++.so.6(_Znwm+0x34)
> > [0x2b21e0581954]
> > > > > > [deb64:03725] [ 9] /usr/lib/libstdc++.so.6(_Znam+0x9)
> > [0x2b21e0581a49]
> > > > > > [deb64:03725] [10]
> > dock6.mpi(_ZN6Orient12match_ligandER7DOCKMol+0x375)
> > > > > > [0x447a85]
> > > > > > [deb64:03725] [11] dock6.mpi(main+0xaf5) [0x42cc75]
> > > > > > [deb64:03725] [12] /lib/libc.so.6(__libc_start_main+0xda)
> > > > [0x2b21e0a054ca]
> > > > > > [deb64:03725] [13] dock6.mpi(__gxx_personality_v0+0xc2) [0x41b4ea]
> > > > > > [deb64:03725] *** End of error message ***
> > > > > > mpirun noticed that job rank 0 with PID 3724 on node deb64 exited
> on
> > > > signal
> > > > > > 15
> > > > > > (Terminated).
> > > > > > 3 additional processes aborted (not shown).
> > > > > >
> > > > > > File rigid.out showed correct reading of grid.nrg.
> > > > > >
> > > > > > _______
> > > > > > The procedure failed also on serial run with
> > > > > >
> > > > > > dock6 -i rigid.in -o rigid.out 2>&1 screen_serial.out
> > > > > >
> > > > > > screen_serial.out:
> > > > > >
> > > > > > terminate called after throwing an instance of 'std::bad_alloc'
> > > > > > waht(): St9bad_alloc
> > > > > >
> > > > > >
> > > > > > i.e, as it was already clear from the above, not a problem of mpi.
> > > > > >
> > > > > > ______
> > > > > >
> > > > > > I understand to be largely out of the main stream of docking
> > procedures
> > > > (and
> > > > > > probably scope). Nonetheless, I am interested in how these large
> > ligands
> > > > > > behave. Therefore, how could I manage to compare the above ligands
> of
> > > > various
> > > > > > size?. I am wondering about changing the grid space and see if
> > docking
> > > > with
> > > > > > the
> > > > > > smaller ligands changes much or not. If OK I could try the larger
> > ligands
> > > > > > with
> > > > > > the new grid. Any better idea? I am not considering to work without
> a
> > > > grid
> > > > > > because I want to compare several molecules. So far I used defaults
> > from
> > > > > > tutorials, i.e. for grid.in:
> > > > > >
> > > > > > compute_grids                  yes
> > > > > > grid_spacing                   0.3
> > > > > > output_molecule                no
> > > > > > contact_score                  no
> > > > > > energy_score                   yes
> > > > > > energy_cutoff_distance         9999
> > > > > > atom_model                     a
> > > > > > attractive_exponent            6
> > > > > > repulsive_exponent             12
> > > > > > distance_dielectric            yes
> > > > > > dielectric_factor              4
> > > > > > bump_filter                    yes
> > > > > > bump_overlap                   0.75
> > > > > > receptor_file    /home/francesco/dockwork/grid/myprotein.mol2
> > > > > > box_file            /home/francesco/dockwork/grid/rec_box.pdb
> > > > > > vdw_definition_file
> /usr/local/dock6/parameters/vdw_AMBER_parm99.defn
> > > > > > score_grid_prefix              grid
> > > > > >
> > > > > >
> > > > > > All that was carried out using A. Magis' sphgen_cpp and
> > sphere_select.
> > > > > >
> > > > > > Thanks
> > > > > >
> > > > > > francesco pietra
> > > >
> > >
> > >
> > >
> > >      
> >
>
____________________________________________________________________________________
> > > Be a better sports nut!  Let your teams follow you
> > > with Yahoo Mobile. Try it now. 
> > http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ
> > >
> > 
> > 
> 
> 
> 
>      
>
____________________________________________________________________________________
> Never miss a thing.  Make Yahoo your home page. 
> http://www.yahoo.com/r/hs
> 



      ____________________________________________________________________________________
Never miss a thing.  Make Yahoo your home page. 
http://www.yahoo.com/r/hs

From chiendarret at yahoo.com  Thu Dec 20 10:11:54 2007
From: chiendarret at yahoo.com (Francesco Pietra)
Date: Thu, 20 Dec 2007 10:11:54 -0800 (PST)
Subject: [Dock-fans] Citation
Message-ID: <805571.35457.qm@web57607.mail.re1.yahoo.com>

I was unable to find recommended citation of DOCK 6.1.

Thanks for providing the citation

francesco pietra


      ____________________________________________________________________________________
Never miss a thing.  Make Yahoo your home page. 
http://www.yahoo.com/r/hs

From jji at cgl.ucsf.edu  Thu Dec 20 10:30:38 2007
From: jji at cgl.ucsf.edu (John J. Irwin)
Date: Thu, 20 Dec 2007 10:30:38 -0800
Subject: [Dock-fans] Citation
In-Reply-To: <805571.35457.qm@web57607.mail.re1.yahoo.com>
References: <805571.35457.qm@web57607.mail.re1.yahoo.com>
Message-ID: <476AB4CE.2000908@cgl.ucsf.edu>

Please use the DOCK 5 reference:

*Moustakas DT*
<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Moustakas%20DT%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus>,
*Lang PT*
<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Lang%20PT%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus>,
*Pegg S*
<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Pegg%20S%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus>,
*Pettersen E*
<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Pettersen%20E%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus>,
*Kuntz ID*
<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Kuntz%20ID%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus>,
*Brooijmans N*
<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Brooijmans%20N%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus>,
*Rizzo RC*
<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Rizzo%20RC%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus>.
J Comput Aided Mol Des. <javascript:AL_get(this, 'jour', 'J Comput Aided
Mol Des.');> 2006 Oct-Nov;20(10-11):601-19. Epub 2006 Dec 6.Click here
to read
<http://www.ncbi.nlm.nih.gov/entrez/utils/fref.fcgi?PrId=3055&itool=AbstractPlus-def&uid=17149653&db=pubmed&url=http://dx.doi.org/10.1007/s10822-006-9060-4>

Yes, there are additional features in DOCK 6 vs DOCK 5. These additions
are still unpublished, as far as I know.

John

Francesco Pietra wrote:
> I was unable to find recommended citation of DOCK 6.1.
>
> Thanks for providing the citation
>
> francesco pietra
>
>
>       ____________________________________________________________________________________
> Never miss a thing.  Make Yahoo your home page. 
> http://www.yahoo.com/r/hs
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>   

From ksvinaykumar at gmail.com  Sat Dec 22 09:09:27 2007
From: ksvinaykumar at gmail.com (Vinay Kumar)
Date: Sat, 22 Dec 2007 22:39:27 +0530
Subject: [Dock-fans] installing from source.
Message-ID: <ef4e9c1a0712220909n624ec289kc57b55152feeaab5@mail.gmail.com>

Hi dockers,
I would like to know if anyone has installed dock6 from source on
fedora 6 machine? i tried and came up with some errors. "g77 command
not found".

Regards,
Vinay

From jji at cgl.ucsf.edu  Sat Dec 22 12:51:28 2007
From: jji at cgl.ucsf.edu (John J. Irwin)
Date: Sat, 22 Dec 2007 12:51:28 -0800
Subject: [Dock-fans] installing from source.
In-Reply-To: <ef4e9c1a0712220909n624ec289kc57b55152feeaab5@mail.gmail.com>
References: <ef4e9c1a0712220909n624ec289kc57b55152feeaab5@mail.gmail.com>
Message-ID: <476D78D0.9020600@cgl.ucsf.edu>

you need to install a fortran compiler such as g77.
Did you try yum install g77? or just get the rpm.

Vinay Kumar wrote:
> Hi dockers,
> I would like to know if anyone has installed dock6 from source on
> fedora 6 machine? i tried and came up with some errors. "g77 command
> not found".
>
> Regards,
> Vinay
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>   

From mxs10 at case.edu  Thu Dec 27 11:02:56 2007
From: mxs10 at case.edu (Menachem Shoham)
Date: Thu, 27 Dec 2007 14:02:56 -0500
Subject: [Dock-fans] bad allocation
Message-ID: <9A752536-75B0-4B98-8402-ACBDBA1A5187@case.edu>

We are trying to dock a fairly large ligand to a model receptor  
protein. When I limited the number of spheres, I was able to run a  
rigid docking program, although the docking score was not very good.  
When I tried the same thing with flexible docking, it failed with the  
suggestion of increasing the target area.
When I increased the number of spheres, the rigid docking failed,  
giving a message of "-threw instance of std::bad_alloc".
The grid files are about 10 fold larger than with fewer spheres. Was  
this due to limitation of our computer or was it due to the large size  
of the grid files?

																Barbara Truitt

From javacfish at yahoo.com.cn  Fri Dec 28 06:33:02 2007
From: javacfish at yahoo.com.cn (li bai)
Date: Fri, 28 Dec 2007 22:33:02 +0800 (CST)
Subject: [Dock-fans] Help,How install "install legacy_accessories" of DOCK
Message-ID: <625418.9698.qm@web15003.mail.cnb.yahoo.com>

Hello,everyone!
  I have one problem to solve. The problem is How install " legacy_accessories" of DOCK,I found I can not find the "Makefile" of legacy_accessories.So I can step up them .But the "legacy_accessories"  have many funtions.

Who can help me install the "legacy_accessories"?
Thank you!
Sincerely,
Yours.

       
---------------------------------
??????????????????? 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20071228/73fa9162/attachment.html 

From sudmukh at yahoo.com  Fri Dec 28 23:17:50 2007
From: sudmukh at yahoo.com (Sudipto Mukherjee)
Date: Fri, 28 Dec 2007 23:17:50 -0800 (PST)
Subject: [Dock-fans] bad allocation
Message-ID: <834289.7216.qm@web36707.mail.mud.yahoo.com>

Dear Barbara,

Docking works well with about 50-75
spheres in the binding site. Could you specify how many spheres you are
using? Are all roughly in the binding site? Selecting more spheres
would increase the box size for the grid. The size the grid file
increases roughly as the cube of the box size i.e. proportional to the
volume of the box.

I have tested DOCK successfully with grid
files as large as 800MB on a computer with 2GB RAM . However, if the
grid file is larger than the amount of available memory, memory
allocation errors like the one described is likely.
 
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: Menachem Shoham <mxs10 at case.edu>
To: dock-fans at docking.org
Sent: Friday, December 28, 2007 12:32:56 AM
Subject: [Dock-fans] bad allocation


We are trying to dock a fairly large ligand to a model receptor  
protein. When I limited the number of spheres, I was able to run a  
rigid docking program, although the docking score was not very good.  
When I tried the same thing with flexible docking, it failed with the  
suggestion of increasing the target area.
When I increased the number of spheres, the rigid docking failed,  
giving a message of "-threw instance of std::bad_alloc".
The grid files are about 10 fold larger than with fewer spheres. Was  
this due to limitation of our computer or was it due to the large size
  
of the grid files?

                                                                Barbara
 Truitt
_______________________________________________
Dock-fans mailing list
Dock-fans at docking.org
http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans






      ____________________________________________________________________________________
Looking for last minute shopping deals?  
Find them fast with Yahoo! Search.  http://tools.search.yahoo.com/newsearch/category.php?category=shopping
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20071228/1e8391cc/attachment.html 

From sudmukh at yahoo.com  Sun Dec 30 21:31:02 2007
From: sudmukh at yahoo.com (Sudipto Mukherjee)
Date: Sun, 30 Dec 2007 21:31:02 -0800 (PST)
Subject: [Dock-fans] bad allocation
Message-ID: <299966.56961.qm@web36707.mail.mud.yahoo.com>

Dear Barbara,

If rigid docking works fine with the smaller sphere set (n=84), the grid files are probably fine. 

Flexible docking is a harder sampling problem. Dock quits with the message "Could not complete growth".. etc. when it cannot find any reasonably scored conformation, and this often happens for large, floppy ligands with 7 or more rotatable bonds. In this case, you will have to tweak the sampling parameters in dock. Try disabling the bump filter (this will make docking slower), the clash overlap (may lead to bad ligand conformations), changing the number of orients, min anchor size (=6 is a good idea, but can make things very slow) etc.

Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University
----- Original Message ----
From: Barb Truitt <barbara.truitt at case.edu>
To: Sudipto Mukherjee <sudmukh at yahoo.com>
Sent: Monday, December 31, 2007 12:58:06 AM
Subject: Re: [Dock-fans] bad allocation




Sudipto - That may be the problem. I have 354 spheres in the file that I
had tried to run, using a box with 5 angstrom margins. I was able to get
it to run with the tutorial files, and with a smaller cluster of spheres
for our protein that had only 84 spheres, again using a margin of 5
angstroms when forming the box. The grid.nrg files are very large. Is
that because of the number of spheres or because of the characteristics
of our protein? I tried running dock with a smaller selection of spheres,
but it wasn't that much smaller, so the volume of the box wouldn't have
been much smaller. When I ran flexible docking using the smaller number
of spheres, it failed with the suggestion of increasing the size of the
target. I must have overdone it. I'll try again with a smaller number of
spheres. We have ~1.5 GB RAM. How large were your ligands?

Thanks for your help.


Barbara Truitt


At 02:17 AM 12/29/2007, you wrote:

Dear
Barbara,


Docking works well with about 50-75 spheres in the binding site. Could
you specify how many spheres you are using? Are all roughly in the
binding site? Selecting more spheres would increase the box size for the
grid. The size the grid file increases roughly as the cube of the box
size i.e. proportional to the volume of the box.


I have tested DOCK successfully with grid files as large as 800MB on a
computer with 2GB RAM . However, if the grid file is larger than the
amount of available memory, memory allocation errors like the one
described is likely.

 

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: Menachem Shoham <mxs10 at case.edu>

To: dock-fans at docking.org

Sent: Friday, December 28, 2007 12:32:56 AM

Subject: [Dock-fans] bad allocation


We are trying to dock a fairly large ligand to a model receptor 


protein. When I limited the number of spheres, I was able to run a 


rigid docking program, although the docking score was not very
good.  

When I tried the same thing with flexible docking, it failed with
the  

suggestion of increasing the target area.

When I increased the number of spheres, the rigid docking failed, 


giving a message of "-threw instance of std::bad_alloc".

The grid files are about 10 fold larger than with fewer spheres.
Was  

this due to limitation of our computer or was it due to the large
size   

of the grid files?


                                                               
Barbara Truitt

_______________________________________________

Dock-fans mailing list

Dock-fans at docking.org


http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans






Be a better friend, newshound, and know-it-all with Yahoo! Mobile.

Try it now. 

_______________________________________________

Dock-fans mailing list

Dock-fans at docking.org


http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans






      ____________________________________________________________________________________
Looking for last minute shopping deals?  
Find them fast with Yahoo! Search.  http://tools.search.yahoo.com/newsearch/category.php?category=shopping
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20071230/cbc52001/attachment.html