From wanrui973549 at yahoo.com.cn Mon Jul 2 17:54:00 2007 From: wanrui973549 at yahoo.com.cn (=?gb2312?q?=EE=A3=20=CD=F2?=) Date: Tue, 3 Jul 2007 08:54:00 +0800 (CST) Subject: [Dock-fans] (no subject) Message-ID: <713388.66951.qm@web15003.mail.cnb.yahoo.com> hi: I`m a dock5.4.0_windows user,when I was using the dock.5.4.0_windows, I always encounter the problem: burst error after the program was iniliating the protein.nrg file. would you please fix this problem for me. Thanks a lot. wanrui 2007-07-03 --------------------------------- ????????3.5G???20M??? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070703/041179ca/attachment.html From rima.chaudhuri at gmail.com Tue Jul 3 10:15:53 2007 From: rima.chaudhuri at gmail.com (Rima Chaudhuri) Date: Tue, 3 Jul 2007 12:15:53 -0500 Subject: [Dock-fans] Amber-Score Error Message-ID: <7503b17d0707031015m7377194cydd4efbf211e88e1@mail.gmail.com> Hello! I am trying to rescore a set of 30 molecules using Amber Score of version dock6.1 parallel on a sgi machine. I applied the bugfix2. Post prepare_amber.pl I get the desired files except the lig.1.amber.pdb, lig.1.gaff.mol2 and lig.1.frcmod files for each of the ligands. The script gets me all the required receptor files and complex files(which I doubt is correct, since the ligand files were not written properly). On further investigation I see in the amberize_ligand.1.out file : running: antechamber to generate GAFF mol2 file format with AM1-BCC charges sh: /n4/rima_temp/dock6/bin/bondtype: not found Error: cannot run "/n4/rima_temp/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c properly, exit Running: /n4/rima_temp/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full Cannot open file flex_GRL_charge_ranked.29.gaff.mol2, exit ... ... ... AMBER General Force Field for organic mol., add. info. at the end (June, 2003) Could not open file flex_GRL_charge_ranked.29.frcmod: not found Could not open file flex_GRL_charge_ranked.29.gaff.mol2: not found As a result, it cannot write/read the frcmod and gaff.mol2 files for the ligand. In my dock6/bin directory, the bondtype is bondtype.mpi , also atomtype is atomtype.mpi etc..I tried to look into the amberize_ligand script to see where I could change the 'bondtype' to 'bondtype.mpi' but could not find so...can someone tell me where is the code/codes that needs to be changed? or what should I be doing now? P.S: I changed some names for e.g. antechamber to antechamber.mpi and parmchk to parmchk.mpi and teLeap to teLeap.mpi etc ... Thanks -- -Rima -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070703/5024bb19/attachment.html From sbrozell at scripps.edu Tue Jul 3 10:46:58 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Tue, 3 Jul 2007 10:46:58 -0700 Subject: [Dock-fans] Amber-Score Error In-Reply-To: <7503b17d0707031015m7377194cydd4efbf211e88e1@mail.gmail.com> References: <7503b17d0707031015m7377194cydd4efbf211e88e1@mail.gmail.com> Message-ID: Hi, On Tue, 3 Jul 2007, Rima Chaudhuri wrote: > I am trying to rescore a set of 30 molecules using Amber Score of version > dock6.1 parallel on a sgi machine. I applied the bugfix2. > Post prepare_amber.pl I get the desired files except the lig.1.amber.pdb, > lig.1.gaff.mol2 and lig.1.frcmod files for each of the ligands. > The script gets me all the required receptor files and complex files(which I > doubt is correct, since the ligand files were not written properly). > On further investigation I see in the amberize_ligand.1.out file : > > running: antechamber to generate GAFF mol2 file format with AM1-BCC charges > sh: /n4/rima_temp/dock6/bin/bondtype: not found > Error: cannot run "/n4/rima_temp/dock6/bin/bondtype -i > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in > judgebondtype() of antechamber.c properly, exit > Running: /n4/rima_temp/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o > ANTECHAMBER_BOND_TYPE.AC -f ac -j full > Cannot open file flex_GRL_charge_ranked.29.gaff.mol2, exit > ... > ... > ... > AMBER General Force Field for organic mol., add. info. at the end (June, > 2003) > Could not open file flex_GRL_charge_ranked.29.frcmod: not found > Could not open file flex_GRL_charge_ranked.29.gaff.mol2: not found > > > As a result, it cannot write/read the frcmod and gaff.mol2 files for the > ligand. > In my dock6/bin directory, the bondtype is bondtype.mpi , also atomtype is > atomtype.mpi etc..I tried to look into the amberize_ligand script to see > where I could change the 'bondtype' to 'bondtype.mpi' but could not find > so...can someone tell me where is the code/codes that needs to be changed? > or what should I be doing now? > > P.S: I changed some names for e.g. antechamber to antechamber.mpi and > parmchk to parmchk.mpi and teLeap to teLeap.mpi etc ... Apparently, the mpi suffix is being applied to all executables, not just parallel ones. A workaround is to build serially: cd install make distclean ./configure sgi make install make test Scott From sbrozell at scripps.edu Tue Jul 3 11:03:35 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Tue, 3 Jul 2007 11:03:35 -0700 Subject: [Dock-fans] (no subject) In-Reply-To: <713388.66951.qm@web15003.mail.cnb.yahoo.com> References: <713388.66951.qm@web15003.mail.cnb.yahoo.com> Message-ID: Hi, On Tue, 3 Jul 2007, [gb2312] ?? ?? wrote: > I`m a dock5.4.0_windows user,when I was using the dock.5.4.0_windows, I always encounter the problem: burst error after the program was iniliating the protein.nrg file. would you please fix this problem for me. Thanks a lot. > wanrui The current version of DOCK is 6.1; please upgrade. Terry Lang and others fixed a bunch of bugs from 5.4 to 6.0. What's a burst error; the first hit on goooggggle is http://en.wikipedia.org/wiki/Error_burst If this is appropriate then you should indicate the guard band ;-) Apparently protein.nrg is some user file. Scott From rima.chaudhuri at gmail.com Tue Jul 3 11:38:16 2007 From: rima.chaudhuri at gmail.com (Rima Chaudhuri) Date: Tue, 3 Jul 2007 13:38:16 -0500 Subject: [Dock-fans] Amber-Score Error In-Reply-To: References: <7503b17d0707031015m7377194cydd4efbf211e88e1@mail.gmail.com> Message-ID: <7503b17d0707031138j38cc6981nda68ffce3aefffcf@mail.gmail.com> Hello, I changed the names of bondtype.mpi and atomtype.mpi to bondtype and atomtype, and now that part works but the amberize ligand now gives the following Running: $AMBERHOME/bin/divcon sh: /n1/nprog/amber/amber9/bin/divcon: cannot execute Error: cannot run "$AMBERHOME/bin/divcon" of bcc() in charge.c properly, exit Running: /n4/rima_temp/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full Running: /n4/rima_temp/dock6/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Cannot open file ligand_all.2.gaff.mol2, exit I checked, the divcon file is in the mentioned directory! Any suggestions? Thanks Rima On 7/3/07, Scott Brozell wrote: > > Hi, > > On Tue, 3 Jul 2007, Rima Chaudhuri wrote: > > > I am trying to rescore a set of 30 molecules using Amber Score of > version > > dock6.1 parallel on a sgi machine. I applied the bugfix2. > > Post prepare_amber.pl I get the desired files except the lig.1.amber.pdb > , > > lig.1.gaff.mol2 and lig.1.frcmod files for each of the ligands. > > The script gets me all the required receptor files and complex > files(which I > > doubt is correct, since the ligand files were not written properly). > > On further investigation I see in the amberize_ligand.1.out file : > > > > running: antechamber to generate GAFF mol2 file format with AM1-BCC > charges > > sh: /n4/rima_temp/dock6/bin/bondtype: not found > > Error: cannot run "/n4/rima_temp/dock6/bin/bondtype -i > > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in > > judgebondtype() of antechamber.c properly, exit > > Running: /n4/rima_temp/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 > -o > > ANTECHAMBER_BOND_TYPE.AC -f ac -j full > > Cannot open file flex_GRL_charge_ranked.29.gaff.mol2, exit > > ... > > ... > > ... > > AMBER General Force Field for organic mol., add. info. at the end (June, > > 2003) > > Could not open file flex_GRL_charge_ranked.29.frcmod: not found > > Could not open file flex_GRL_charge_ranked.29.gaff.mol2: not found > > > > > > As a result, it cannot write/read the frcmod and gaff.mol2 files for the > > ligand. > > In my dock6/bin directory, the bondtype is bondtype.mpi , also atomtype > is > > atomtype.mpi etc..I tried to look into the amberize_ligand script to see > > where I could change the 'bondtype' to 'bondtype.mpi' but could not find > > so...can someone tell me where is the code/codes that needs to be > changed? > > or what should I be doing now? > > > > P.S: I changed some names for e.g. antechamber to antechamber.mpi and > > parmchk to parmchk.mpi and teLeap to teLeap.mpi etc ... > > Apparently, the mpi suffix is being applied to all executables, > not just parallel ones. A workaround is to build serially: > > cd install > make distclean > ./configure sgi > make install > make test > > Scott > > -- -Rima -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070703/83c84611/attachment-0001.html From sbrozell at scripps.edu Tue Jul 3 12:00:03 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Tue, 3 Jul 2007 12:00:03 -0700 Subject: [Dock-fans] Amber-Score Error In-Reply-To: <7503b17d0707031138j38cc6981nda68ffce3aefffcf@mail.gmail.com> References: <7503b17d0707031015m7377194cydd4efbf211e88e1@mail.gmail.com> <7503b17d0707031138j38cc6981nda68ffce3aefffcf@mail.gmail.com> Message-ID: Hi, On Tue, 3 Jul 2007, Rima Chaudhuri wrote: > I changed the names of bondtype.mpi and atomtype.mpi to bondtype and > atomtype, and now that part works but the amberize ligand now gives the > following > > Running: $AMBERHOME/bin/divcon > sh: /n1/nprog/amber/amber9/bin/divcon: cannot execute > Error: cannot run "$AMBERHOME/bin/divcon" of bcc() in charge.c properly, > exit > Running: /n4/rima_temp/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o > ANTECHAMBER_BOND_TYPE.AC -f ac -j full > Running: /n4/rima_temp/dock6/bin/atomtype -i ANTECHAMBER_AC.AC0 -o > ANTECHAMBER_AC.AC -p gaff > Cannot open file ligand_all.2.gaff.mol2, exit > > I checked, the divcon file is in the mentioned directory! Not sure what your last sentence means: does /n1/nprog/amber/amber9/bin/divcon exist and is it executable ? Anyway, this is a known problem with antechamber; the solution is to undefine AMBERHOME. Then the DOCK executables will be used. Scott > On 7/3/07, Scott Brozell wrote: > > > > Hi, > > > > On Tue, 3 Jul 2007, Rima Chaudhuri wrote: > > > > > I am trying to rescore a set of 30 molecules using Amber Score of > > version > > > dock6.1 parallel on a sgi machine. I applied the bugfix2. > > > Post prepare_amber.pl I get the desired files except the lig.1.amber.pdb > > , > > > lig.1.gaff.mol2 and lig.1.frcmod files for each of the ligands. > > > The script gets me all the required receptor files and complex > > files(which I > > > doubt is correct, since the ligand files were not written properly). > > > On further investigation I see in the amberize_ligand.1.out file : > > > > > > running: antechamber to generate GAFF mol2 file format with AM1-BCC > > charges > > > sh: /n4/rima_temp/dock6/bin/bondtype: not found > > > Error: cannot run "/n4/rima_temp/dock6/bin/bondtype -i > > > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in > > > judgebondtype() of antechamber.c properly, exit > > > Running: /n4/rima_temp/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 > > -o > > > ANTECHAMBER_BOND_TYPE.AC -f ac -j full > > > Cannot open file flex_GRL_charge_ranked.29.gaff.mol2, exit > > > ... > > > ... > > > ... > > > AMBER General Force Field for organic mol., add. info. at the end (June, > > > 2003) > > > Could not open file flex_GRL_charge_ranked.29.frcmod: not found > > > Could not open file flex_GRL_charge_ranked.29.gaff.mol2: not found > > > > > > > > > As a result, it cannot write/read the frcmod and gaff.mol2 files for the > > > ligand. > > > In my dock6/bin directory, the bondtype is bondtype.mpi , also atomtype > > is > > > atomtype.mpi etc..I tried to look into the amberize_ligand script to see > > > where I could change the 'bondtype' to 'bondtype.mpi' but could not find > > > so...can someone tell me where is the code/codes that needs to be > > changed? > > > or what should I be doing now? > > > > > > P.S: I changed some names for e.g. antechamber to antechamber.mpi and > > > parmchk to parmchk.mpi and teLeap to teLeap.mpi etc ... > > > > Apparently, the mpi suffix is being applied to all executables, > > not just parallel ones. A workaround is to build serially: > > > > cd install > > make distclean > > ./configure sgi > > make install > > make test > > From sbrozell at scripps.edu Tue Jul 3 20:05:55 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Tue, 3 Jul 2007 20:05:55 -0700 Subject: [Dock-fans] dms installation In-Reply-To: <50511.201.86.146.230.1183258483.squirrel@www.redefiocruz.fiocruz.br> References: <50511.201.86.146.230.1183258483.squirrel@www.redefiocruz.fiocruz.br> Message-ID: Hi, On Sat, 30 Jun 2007 lpgomes at fiocruz.br wrote: > I had the following problem in compilation of dms. ANd I would > like to know what to do. > Regards, > Luciano P Gomes > FIOCRUZ Bras?lia > > cd libpdb ; make OPT="-O" > make[1]: Entrando no diret?rio `/usr/dms/libpdb' > make[1]: Nada a ser feito para `all'. > make[1]: Saindo do diret?rio `/usr/dms/libpdb' > cc -DDESTLIB=\"/usr/local/lib/dms/\" > -DSERVER_PATH=\"/usr/local/lib/dms/dmsd\" -Ilibpdb -O -c -o > input.o input.c > input.c: In function ?read_pdb?: > input.c:104: warning: incompatible implicit declaration of > built-in function ?strcpy? > input.c:104: error: too many arguments to function ?strcpy? > input.c:105: error: too many arguments to function ?strcpy? > input.c:113: warning: incompatible implicit declaration of > built-in function ?strncat? > input.c:151: warning: incompatible implicit declaration of > built-in function ?exit? ... It appears that the header file declarations of these functions, strcpy, exit, etc, are not being presented to the compiler. This is suspicious since input.c contains: ... #include #include #include #include ... In addition, the errors above attributed to strcpy are actually scopy function calls according to my version of input.c. Here are some debugging ideas: Verify that your input.c is verbatim from your dms distribution and that it contains those includes starting at line 33. Get the preprocessor output via cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=\"/usr/local/lib/dms/dmsd\" -Ilibpdb -E input.c and look for the declarations of the above functions and see whats happening on line 104 with regard to scopy. Try to disable builtins via this compiler option: -fno-builtins If you need more help then send explicit and verbose details including OS and compiler versions, the -E output, the effect of -fno-builtins, etc. Scott From leszek.dobrowolski at gmail.com Wed Jul 4 02:42:41 2007 From: leszek.dobrowolski at gmail.com (Leszek Dobrowolski) Date: Wed, 4 Jul 2007 11:42:41 +0200 Subject: [Dock-fans] A problem with showbox Message-ID: <7e953dba0707040242k42115c39xe2c1174ebd3def24@mail.gmail.com> Hello! I have a problem with showbox (in the DOCK 6.1 package) after executing $ showbox < box.in I get a following error: (...) sphere file- cluster number- fmt: end of file apparent state: unit 1 named ./selected_spheres.sph last format: (a80) lately reading sequential formatted external IO Aborted (core dumped) My "box.in" looks like this: Y 5 ./selected_spheres.sph 1 selected_cluster_box.pdb Have you got any ideas, what's wrong with it? What is "(a80)" ? Best regards, Leszek leszek.dobrowolski at gmail.com From sbrozell at scripps.edu Wed Jul 4 11:09:21 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Wed, 4 Jul 2007 11:09:21 -0700 Subject: [Dock-fans] A problem with showbox In-Reply-To: <7e953dba0707040242k42115c39xe2c1174ebd3def24@mail.gmail.com> References: <7e953dba0707040242k42115c39xe2c1174ebd3def24@mail.gmail.com> Message-ID: Hi, On Wed, 4 Jul 2007, Leszek Dobrowolski wrote: > I have a problem with showbox (in the DOCK 6.1 package) > > $ showbox < box.in > > (...) > sphere file- > cluster number- > fmt: end of file > apparent state: unit 1 named ./selected_spheres.sph > last format: (a80) > lately reading sequential formatted external IO > Aborted (core dumped) > > My "box.in" looks like this: > Y > 5 > ./selected_spheres.sph > 1 > selected_cluster_box.pdb > > > Have you got any ideas, what's wrong with it? What is "(a80)" ? The header lines of ./selected_spheres.sph are faulty. Verify that the file contains a line like this cluster 1 number of spheres in cluster 12 and compare your sphere file to install/test/grid_generation/struct.sph a80 is a character data edit descriptor http://www.fortran.com/F77_std/rjcnf0001-sh-13.html#sh-13.5.11 Searching src/accessories/showbox.f for a80 find only one line; take a look. Scott From sbrozell at scripps.edu Wed Jul 4 22:42:18 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Wed, 4 Jul 2007 22:42:18 -0700 Subject: [Dock-fans] Using sphgen and dms????? In-Reply-To: <000801c7b72f$7f27d010$8c4b5c82@bender> References: <000801c7b72f$7f27d010$8c4b5c82@bender> Message-ID: Hi, On Mon, 25 Jun 2007, Mathias Baumann wrote: > I'm using cygwin on XP and got as far as the installation of dms where i had the problems with the LIB & BINPATH as some other people here but worked around it by setting these pathnames to the propper directory. Now however i wanted to use the sphgen command for the 2nd step of the tutorial but it always kept telling me that there was no such command. By using the explorer i found that there was no sphgen.exe in the bin-library of my cygwin folder but instead it was in my dock6/bin folder. so i used BINPATH again to set it to the dock6 directory and now sphgen works. > > To make a long story short, do i always have to change my BIN-directory to use dock? coz i tried to reinstall it by first setting the BIN & LIBPATH but it will install into the dock folder anyway and not in my home directory. I'm new to linux and cygwin so i figured all of this by trial and error but maybe i'm missing something important and someone can tell me what i'm doing wrong. > I do not use cygwin and a few minutes ggooooooggggggling and at the cygwin home page http://www.cygwin.com/ and the cygwin mailing list http://cygwin.com/ml/cygwin/ did not find any good hits. dock6/bin is the canonical path for DOCK executables. The Makefiles use a macro for this. The configuration files define the macro SFX for the suffix for executables. This was originally used in Amber as a way to add an exe extension under cygwin, but was hijacked in DOCK for mpi and pbsa extensions for alternate dock6 executables. One could create a config.h that has SFX=.exe. So DOCK seems to have enough flexibility to accommodate your scenario with some under the hood work. However, perhaps a cygwin user/expert can comment on the appropriateness of your scenario. Scott From case at scripps.edu Thu Jul 5 23:29:17 2007 From: case at scripps.edu (David A. Case) Date: Thu, 5 Jul 2007 23:29:17 -0700 Subject: [Dock-fans] Using sphgen and dms????? In-Reply-To: References: <000801c7b72f$7f27d010$8c4b5c82@bender> Message-ID: <20070706062917.GA4584@scripps.edu> On Wed, Jul 04, 2007, Scott Brozell wrote: > > > I'm using cygwin on XP and got as far as the installation of dms where i > > had the problems with the LIB & BINPATH as some other people here but > > worked around it by setting these pathnames to the propper directory. Now > > however i wanted to use the sphgen command for the 2nd step of the > > tutorial but it always kept telling me that there was no such command. By > > using the explorer i found that there was no sphgen.exe in the bin-library > > of my cygwin folder but instead it was in my dock6/bin folder. so i used > > BINPATH again to set it to the dock6 directory and now sphgen works. Apologies if I'm coming in late here, and missed something earlier. The sphgen.exe file *should* in dock6/bin. You should set your PATH variable by putting something like this into your /home/username/.bashrc file: export PATH=/usr/local/bin:/bin:/usr/X11R6/bin:/home/username/dock6/bin (assuming you installed dock6 under your home directory; if not, insert the correct path above). Then, everytime to start a cygwin shell, the system will know to look in both /bin and in /home/username/dock6/bin when it wants to find executables. You can have many directories in the $PATH variable, separated by colons. Since you say you are new to linux and cygwin, I'm hoping that maybe this will help. Please accept my apologies if this is stuff you already know. ...good luck....dave case From rima.chaudhuri at gmail.com Fri Jul 6 15:03:44 2007 From: rima.chaudhuri at gmail.com (Rima Chaudhuri) Date: Fri, 6 Jul 2007 17:03:44 -0500 Subject: [Dock-fans] Amber score Message-ID: <7503b17d0707061503lc7dca2cm479702b53448fa4b@mail.gmail.com> Hello, I am running 2 different sets of ligand conformations ( but of the same 30 molecules) for rescoring with amber_score. A. Using the normal grid score to rank some 30 compound and then use these conformations for rescoring with amberscore.I used the movable region as 'ligand' in case1 and 'distance' in case2. Case 1 runs fine. Case 2 however, stalls at the following point Molecule Library Output Parameters ------------------------------------------------------------------------------------------ ligand_outfile_prefix out_dist write_orientations no num_scored_conformers_written 1 rank_ligands yes max_ranked_ligands 30 these are the last few lines of the dock.out file, it is still running and has been for the past 2.5 hrs w/o writing anything else. I want to know if this is normal? I used the pre-md min steps as 100, md-steps of 5000 and post md steps of 100. The movable cutoff was specified as 8.0 angstroms, temperature 300K...any suggestions? B. Using the same ligand set as in 1, I first ran them in GOLD and used these conformations to re-score in dock_amber_score. Almost all the amber scores are positive, whereas in the case of using grid score and then amber re-scoring the amber scores were all negative values and suggested good binding as expected. I understand that using the gold conformations and then dock might cause this problem due to differences in energy terms and parameters between Gold and dock_amber_score, but to keep things consistent, is there a workaround this issue? meaning , if I wanted to make correlation plots between the amberscore and experimental data, right now it is quite fruitless! If I stick to the conformations from grid_score ranking, the do not look so good and the experimental correlation is only 18%. I would rather want to have the gold conformations as the starting geometry! any suggestions that can help me get non-positive binding energy using amber_score? Thanks -- -Rima -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070706/9acfd526/attachment.html From sbrozell at scripps.edu Fri Jul 6 15:49:24 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Fri, 6 Jul 2007 15:49:24 -0700 Subject: [Dock-fans] Amber score In-Reply-To: <7503b17d0707061503lc7dca2cm479702b53448fa4b@mail.gmail.com> References: <7503b17d0707061503lc7dca2cm479702b53448fa4b@mail.gmail.com> Message-ID: Hi, On Fri, 6 Jul 2007, Rima Chaudhuri wrote: > I am running 2 different sets of ligand conformations ( but of the same 30 > molecules) for rescoring with amber_score. > > A. Using the normal grid score to rank some 30 compound and then use these > conformations for rescoring with amberscore.I used the movable region as > 'ligand' in case1 and 'distance' in case2. Case 1 runs fine. Case 2 however, > stalls at the following point > > Molecule Library Output Parameters > ------------------------------------------------------------------------------------------ > ligand_outfile_prefix out_dist > write_orientations no > num_scored_conformers_written 1 > rank_ligands yes > max_ranked_ligands 30 > > these are the last few lines of the dock.out file, it is still running and > has been for the past 2.5 hrs w/o writing anything else. I want to know if > this is normal? I used the pre-md min steps as 100, md-steps of 5000 and > post md steps of 100. The movable cutoff was specified as 8.0 angstroms, > temperature 300K...any suggestions? The only extra input parameter for distance movable vs ligand movable is receptor_site_file. Did you specify it ? For details see http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore distance may be a lot slower than ligand. As usual, the advice is to run in verbose mode when doing something for the first time: dock -v bla bla A lot of extra info will be emitted; it will include clues on the computational intensivity. > B. Using the same ligand set as in 1, I first ran them in GOLD and used > these conformations to re-score in dock_amber_score. Almost all the amber > scores are positive, whereas in the case of using grid score and then amber > re-scoring the amber scores were all negative values and suggested good > binding as expected. I understand that using the gold conformations and then > dock might cause this problem due to differences in energy terms and > parameters between Gold and dock_amber_score, but to keep things consistent, > is there a workaround this issue? meaning , if I wanted to make correlation > plots between the amberscore and experimental data, right now it is quite > fruitless! > > If I stick to the conformations from grid_score ranking, the do not look so > good and the experimental correlation is only 18%. I would rather want to > have the gold conformations as the starting geometry! any suggestions that > can help me get non-positive binding energy using amber_score? These are interesting issues perhaps on the bleeding edge of docking; I am not aware of any study of them. How do the other DOCK scores fair on the GOLD conformations ? I cannot think of any cheap black box workarounds. Increasing the movable region size may improve the amber scores. One would expect that more receptor preparation would improve the amber scores. As mentioned before the error bars on binding energies from docking are large: http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-March/000973.html Good luck and keep us posted, Scott From al.s.nascimento at gmail.com Mon Jul 9 10:16:54 2007 From: al.s.nascimento at gmail.com (Alessandro Nascimento) Date: Mon, 9 Jul 2007 14:16:54 -0300 Subject: [Dock-fans] failure on dock.mpi Message-ID: <86ad38fa0707091016j29035fe8vf101460bfefd3ea7@mail.gmail.com> Hi dock users, I'm new to dock and also to molecular docking... I took a look at the tutorials, and I am trying to do my first dock using a database (zinc). When running dock in a single processor, my job works fine. When I try it in parallel (5 processors, mpich2), i get the following error [cli_1]: rank 0 in job 8 ruska_37276 caused collective abort of all ranks exit status of rank 0: killed by signal 11 I pasted my dock input file below. Any clue to this problem? ligand_atom_file zinc.mol2 limit_max_ligands yes max_ligands 100 skip_molecule no read_mol_solvation no calculate_rmsd no orient_ligand yes automated_matching yes receptor_site_file rec.sph max_orientations 120000 critical_points yes chemical_matching yes chem_match_tbl /home/apps/dock/dock6/parameters/chem_match.tbl use_ligand_spheres no flexible_ligand no bump_filter no score_molecules yes contact_score_primary no contact_score_secondary no 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 grid dock3.5_score_secondary no continuous_score_secondary yes cont_score_rec_filename rec_charged.mol2 cont_score_att_exp 6 cont_score_rep_exp 12 cont_score_rep_rad_scale 1 cont_score_dielectric 4.0 cont_score_vdw_scale 1 cont_score_es_scale 1 minimize_ligand yes simplex_max_iterations 1000 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_final_min no simplex_secondary_minimize_pose yes use_advanced_secondary_simplex_parameters no simplex_secondary_max_iterations 100 simplex_secondary_min_add_internal no simplex_random_seed 0 atom_model all vdw_defn_file /home/apps/dock/dock6/parameters/vdw_AMBER_parm99.defn flex_defn_file /home/apps/dock/dock6/parameters/flex.defn flex_drive_file /home/apps/dock/dock6/parameters/flex_drive.tbl chem_defn_file /home/apps/dock/dock6/parameters/chem.defn ligand_outfile_prefix flex write_orientations no num_primary_scored_conformers_rescored 4 cluster_primary_conformations yes cluster_rmsd_threshold 2.0 num_clusterheads_for_rescore 5 num_secondary_scored_conformers_written 4 rank_primary_ligands no max_primary_ranked 10 rank_secondary_ligands no max_secondary_ranked 10 -- [ ]s --alessandro From sbrozell at scripps.edu Mon Jul 9 14:22:03 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Mon, 9 Jul 2007 14:22:03 -0700 Subject: [Dock-fans] failure on dock.mpi In-Reply-To: <86ad38fa0707091016j29035fe8vf101460bfefd3ea7@mail.gmail.com> References: <86ad38fa0707091016j29035fe8vf101460bfefd3ea7@mail.gmail.com> Message-ID: Hi, On Mon, 9 Jul 2007, Alessandro Nascimento wrote: > I'm new to dock and also to molecular docking... > I took a look at the tutorials, and I am trying to do my first dock > using a database (zinc). > When running dock in a single processor, my job works fine. When I try > it in parallel (5 processors, mpich2), i get the following error > > [cli_1]: rank 0 in job 8 ruska_37276 caused collective abort of all ranks > exit status of rank 0: killed by signal 11 > > I pasted my dock input file below. Any clue to this problem? The error above is a generic one from MPI. Did you look for clues in the dock output ? What happens with 1, 2, or 3 numbers of processors ? Did the dock6/install/test/mpi quality control regression test pass ? Retry it: cd dock6/install/test/mpi make clean make Can you run other MPI programs ? Scott > ligand_atom_file zinc.mol2 > limit_max_ligands yes > max_ligands 100 > skip_molecule no > read_mol_solvation no > calculate_rmsd no > orient_ligand yes > automated_matching yes > receptor_site_file rec.sph > max_orientations 120000 > critical_points yes > chemical_matching yes > chem_match_tbl > /home/apps/dock/dock6/parameters/chem_match.tbl > use_ligand_spheres no > flexible_ligand no > bump_filter no > score_molecules yes > contact_score_primary no > contact_score_secondary no > 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 grid > dock3.5_score_secondary no > continuous_score_secondary yes > cont_score_rec_filename rec_charged.mol2 > cont_score_att_exp 6 > cont_score_rep_exp 12 > cont_score_rep_rad_scale 1 > cont_score_dielectric 4.0 > cont_score_vdw_scale 1 > cont_score_es_scale 1 > minimize_ligand yes > simplex_max_iterations 1000 > 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_final_min no > simplex_secondary_minimize_pose yes > use_advanced_secondary_simplex_parameters no > simplex_secondary_max_iterations 100 > simplex_secondary_min_add_internal no > simplex_random_seed 0 > atom_model all > vdw_defn_file > /home/apps/dock/dock6/parameters/vdw_AMBER_parm99.defn > flex_defn_file > /home/apps/dock/dock6/parameters/flex.defn > flex_drive_file > /home/apps/dock/dock6/parameters/flex_drive.tbl > chem_defn_file > /home/apps/dock/dock6/parameters/chem.defn > ligand_outfile_prefix flex > write_orientations no > num_primary_scored_conformers_rescored 4 > cluster_primary_conformations yes > cluster_rmsd_threshold 2.0 > num_clusterheads_for_rescore 5 > num_secondary_scored_conformers_written 4 > rank_primary_ligands no > max_primary_ranked 10 > rank_secondary_ligands no > max_secondary_ranked 10 From al.s.nascimento at gmail.com Mon Jul 9 15:32:42 2007 From: al.s.nascimento at gmail.com (Alessandro Nascimento) Date: Mon, 9 Jul 2007 19:32:42 -0300 Subject: [Dock-fans] failure on dock.mpi In-Reply-To: References: <86ad38fa0707091016j29035fe8vf101460bfefd3ea7@mail.gmail.com> Message-ID: <86ad38fa0707091532u87eef91me6ffcef96e63d491@mail.gmail.com> On 7/9/07, Scott Brozell wrote: > The error above is a generic one from MPI. > Did you look for clues in the dock output ? Yes, I did, but there is no information. The output file is truncated. One molecule was docked and the file finished without any information.... > What happens with 1, 2, or 3 numbers of processors ? > With 3 and 2 processors the same error occurs at the same moment (first molecule being docked). In a single processor (mpirun -np1 dock.mpi ) the job is running fine (at least until this moment)... 3 molecules have already being docked > Did the dock6/install/test/mpi quality control regression test pass ? > Retry it: > cd dock6/install/test/mpi > make clean > make I did it again and pasted below the results. I failed, but without any mpi messages (to my best knowledge, at least ;) !!!! ) > > Can you run other MPI programs ? > > Scott > I run amber over lam-mpi. I'm not experienced with mpich2. Maybe I might be doing something wrong! By this poor report, can you have any idea of what might be happening? Thanks a lot, one more time! make[1]: Entering directory `/home/apps/dock/dock6/install/test/mpi' cd ../grid_generation && make test make[2]: Entering directory `/home/apps/dock/dock6/install/test/grid_generation' # Construct box to enclose spheres ../../../bin/showbox < box.in > /dev/null ../dockdif box.pdb.save box.pdb diffing box.pdb.save with box.pdb PASSED ============================================================== # Compute scoring grids ../../../bin/grid -i grid.in -o grid.out ../dockdif grid.out.save grid.out diffing grid.out.save with grid.out PASSED ============================================================== make[2]: Leaving directory `/home/apps/dock/dock6/install/test/grid_generation' make[1]: Leaving directory `/home/apps/dock/dock6/install/test/mpi' make[1]: Entering directory `/home/apps/dock/dock6/install/test/mpi' Processing test mpi /home/apps/mpich2/bin/mpirun -np 2 ../../../bin/dock6.mpi -i mpi.dockin -o mpi.dockmpiout Initializing MPI Routines... Initializing MPI Routines... ../dockdif -t 8 mpi.dockmpiout.save mpi.dockmpiout diffing mpi.dockmpiout.save with mpi.dockmpiout possible FAILURE: check mpi.dockmpiout.dif ============================================================== diffing mpi_ranked.mol2.save with mpi_ranked.mol2 possible FAILURE: check mpi_ranked.mol2.dif ============================================================== make[1]: Leaving directory `/home/apps/dock/dock6/install/test/mpi' more mpi.dockmpiout.dif : 106c106 < Conformations: 3 --- > Conformations: 4 110a111,118 > Molecule: ZINC01555236 > Anchors: 1 > Orientations: 50 > Conformations: 18 > Grid Score: 501606144. > vdw: 501606144. > es: -10. > ----------------------------------- 114,117c122,125 < Conformations: 6 < Grid Score: 21. < vdw: 19. < es: 1. --- > Conformations: 7 > Grid Score: -12. > vdw: -12. > es: -0. 123,125c131,133 < Grid Score: 19. < vdw: 20. < es: -1. --- > Grid Score: 30. > vdw: 32. > es: -2. 130,133c138,141 < Conformations: 48 < Grid Score: -15. < vdw: -13. < es: -1. --- > Conformations: 44 > Grid Score: -12. > vdw: -12. > es: -0. 138c146 < Conformations: 12 --- > Conformations: 16 146,148c154,156 < Conformations: 6 < Grid Score: 145519. < vdw: 145519. --- > Conformations: 2 > Grid Score: 168506. > vdw: 168506. 154c162 < Conformations: 28 --- > Conformations: 29 -- [ ]s --alessandro From u9909930 at uel.ac.uk Tue Jul 10 05:46:32 2007 From: u9909930 at uel.ac.uk (Susan MILLER) Date: Tue, 10 Jul 2007 13:46:32 +0100 Subject: [Dock-fans] Installing Dock6... Message-ID: I'm new to unix/linux, new like novice!!! I'm more of an exe person. I've got a copy of dock6, how do I install it on Linux (fedora bash shell)????? So far I've tar the file, beyond that point I'm hopeless... Can anyone help? Please make the explanation simple... PS: Windows installation would also be helpful since I now have a copy of cygwin. Thanks Susan From jji at cgl.ucsf.edu Tue Jul 10 09:09:36 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Tue, 10 Jul 2007 09:09:36 -0700 Subject: [Dock-fans] Installing Dock6... In-Reply-To: References: Message-ID: <4693AF40.6070400@cgl.ucsf.edu> Hi Susan Have you tried looking at the installation guide? http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Installation Good luck! John Susan MILLER wrote: > I'm new to unix/linux, new like novice!!! I'm more of an exe person. > > I've got a copy of dock6, how do I install it on Linux (fedora bash > shell)????? So far I've tar the file, beyond that point I'm hopeless... Can > anyone help? Please make the explanation simple... > > > > PS: Windows installation would also be helpful since I now have a copy of > cygwin. > > > > Thanks > > > > Susan > > > > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > From al.s.nascimento at gmail.com Tue Jul 10 12:51:32 2007 From: al.s.nascimento at gmail.com (Alessandro Nascimento) Date: Tue, 10 Jul 2007 16:51:32 -0300 Subject: [Dock-fans] failure on dock.mpi In-Reply-To: <86ad38fa0707091532u87eef91me6ffcef96e63d491@mail.gmail.com> References: <86ad38fa0707091016j29035fe8vf101460bfefd3ea7@mail.gmail.com> <86ad38fa0707091532u87eef91me6ffcef96e63d491@mail.gmail.com> Message-ID: <86ad38fa0707101251g1e7570dcw816f310f18fb5ee3@mail.gmail.com> Hi Scottt and Dock-fans, using the same mpich implementation I compiled pmemd (software of particle mesh ewald implementation in amber 9). It is running okay in my cluster now on the 5 nodes (6 processors). However, neither dock parallel tests or my own dock run there.... Just to mention, my machines are Intel Xeon 64 (3.4Ghz), in a Gigabit network (I don't know if hardware issue matter in this kind of problems). As was mentioned, it may be a mpi problem rather than dock problems. I just would like to know if has anyone else seen the same problem.... Thanks in advance one more time!!!!! -alessandro Initializing MPI Routines... Initializing MPI Routines... Initializing MPI Routines... Initializing MPI Routines... tail -f rigid.out cluster_rmsd_threshold 2.0 num_clusterheads_for_rescore 5 num_secondary_scored_conformers_written 4 rank_primary_ligands no rank_secondary_ligands no Initializing Library File Routines... Initializing Orienting Routines... Initializing Grid Score Routines... Reading the energy grid from grid.nrg [cli_1]: aborting job: Fatal error in MPI_Recv: Other MPI error, error stack: MPI_Recv(186).............................: MPI_Recv(buf=0x7fffffc48f1c, count=2, MPI_INT, src=0, tag=100, MPI_COMM_WORLD, status=0x7fffffc46620) failed MPIDI_CH3_Progress_wait(212)..............: an error occurred while handling an event returned by MPIDU_Sock_Wait() MPIDI_CH3I_Progress_handle_sock_event(413): MPIDU_Socki_handle_read(633)..............: connection failure (set=0,sock=1,errno=104:Connection reset by peer) rank 0 in job 6 ruska_34405 caused collective abort of all ranks exit status of rank 0: killed by signal 11 ----------------------------------- Molecule: ZINC00000012 Anchors: 1 Orientations: 120000 Conformations: 2375 Primary Score [2] Exit 11 /home/apps/mpich2/bin/mpiexec -n 5 /home/apps/dock/dock6/bin/dock6.mpi -i rigid.in -o rigid.out wrote: > On 7/9/07, Scott Brozell wrote: > > The error above is a generic one from MPI. > > Did you look for clues in the dock output ? > > Yes, I did, but there is no information. The output file is truncated. > One molecule was docked and the file finished without any > information.... > > > What happens with 1, 2, or 3 numbers of processors ? > > > > With 3 and 2 processors the same error occurs at the same moment > (first molecule being docked). In a single processor (mpirun -np1 > dock.mpi ) the job is running fine (at least until this moment)... 3 > molecules have already being docked > > > Did the dock6/install/test/mpi quality control regression test pass ? > > Retry it: > > cd dock6/install/test/mpi > > make clean > > make > > I did it again and pasted below the results. I failed, but without any > mpi messages (to my best knowledge, at least ;) !!!! ) > > > > > Can you run other MPI programs ? > > > > Scott > > > > I run amber over lam-mpi. I'm not experienced with mpich2. Maybe I > might be doing something wrong! > > By this poor report, can you have any idea of what might be happening? > > Thanks a lot, one more time! > > > > make[1]: Entering directory `/home/apps/dock/dock6/install/test/mpi' > cd ../grid_generation && make test > make[2]: Entering directory `/home/apps/dock/dock6/install/test/grid_generation' > # Construct box to enclose spheres > ../../../bin/showbox < box.in > /dev/null > ../dockdif box.pdb.save box.pdb > diffing box.pdb.save with box.pdb > PASSED > ============================================================== > # Compute scoring grids > ../../../bin/grid -i grid.in -o grid.out > ../dockdif grid.out.save grid.out > diffing grid.out.save with grid.out > PASSED > ============================================================== > make[2]: Leaving directory `/home/apps/dock/dock6/install/test/grid_generation' > make[1]: Leaving directory `/home/apps/dock/dock6/install/test/mpi' > make[1]: Entering directory `/home/apps/dock/dock6/install/test/mpi' > > Processing test mpi > /home/apps/mpich2/bin/mpirun -np 2 ../../../bin/dock6.mpi -i > mpi.dockin -o mpi.dockmpiout > Initializing MPI Routines... > Initializing MPI Routines... > ../dockdif -t 8 mpi.dockmpiout.save mpi.dockmpiout > diffing mpi.dockmpiout.save with mpi.dockmpiout > possible FAILURE: check mpi.dockmpiout.dif > ============================================================== > diffing mpi_ranked.mol2.save with mpi_ranked.mol2 > possible FAILURE: check mpi_ranked.mol2.dif > ============================================================== > make[1]: Leaving directory `/home/apps/dock/dock6/install/test/mpi' > > > more mpi.dockmpiout.dif : > > > 106c106 > < Conformations: 3 > --- > > Conformations: 4 > 110a111,118 > > Molecule: ZINC01555236 > > Anchors: 1 > > Orientations: 50 > > Conformations: 18 > > Grid Score: 501606144. > > vdw: 501606144. > > es: -10. > > ----------------------------------- > 114,117c122,125 > < Conformations: 6 > < Grid Score: 21. > < vdw: 19. > < es: 1. > --- > > Conformations: 7 > > Grid Score: -12. > > vdw: -12. > > es: -0. > 123,125c131,133 > < Grid Score: 19. > < vdw: 20. > < es: -1. > --- > > Grid Score: 30. > > vdw: 32. > > es: -2. > 130,133c138,141 > < Conformations: 48 > < Grid Score: -15. > < vdw: -13. > < es: -1. > --- > > Conformations: 44 > > Grid Score: -12. > > vdw: -12. > > es: -0. > 138c146 > < Conformations: 12 > --- > > Conformations: 16 > 146,148c154,156 > < Conformations: 6 > < Grid Score: 145519. > < vdw: 145519. > --- > > Conformations: 2 > > Grid Score: 168506. > > vdw: 168506. > 154c162 > < Conformations: 28 > --- > > Conformations: 29 > > > > -- > [ ]s > > --alessandro > -- [ ]s --alessandro From sbrozell at scripps.edu Tue Jul 10 13:15:20 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Tue, 10 Jul 2007 13:15:20 -0700 Subject: [Dock-fans] failure on dock.mpi In-Reply-To: <86ad38fa0707091532u87eef91me6ffcef96e63d491@mail.gmail.com> References: <86ad38fa0707091016j29035fe8vf101460bfefd3ea7@mail.gmail.com> <86ad38fa0707091532u87eef91me6ffcef96e63d491@mail.gmail.com> Message-ID: Hi, On Mon, 9 Jul 2007, Alessandro Nascimento wrote: > On 7/9/07, Scott Brozell wrote: > > The error above is a generic one from MPI. > > Did you look for clues in the dock output ? > > Yes, I did, but there is no information. The output file is truncated. > One molecule was docked and the file finished without any > information.... If one molecule was docked then there probably is not a problem with the input file. Is the parallel dock input file the same as your successful serial run ? > > What happens with 1, 2, or 3 numbers of processors ? > > With 3 and 2 processors the same error occurs at the same moment > (first molecule being docked). In a single processor (mpirun -np1 > dock.mpi ) the job is running fine (at least until this moment)... 3 > molecules have already being docked What type of cluster is your machine; how many procs per node ? What type of file system ? > > Did the dock6/install/test/mpi quality control regression test pass ? > > Retry it: > > cd dock6/install/test/mpi > > make clean > > make > > I did it again and pasted below the results. I failed, but without any > mpi messages (to my best knowledge, at least ;) !!!! ) The diffs do not appear to be significant - at least not for the purpose of validating mpi. Rerun the test with more procs, ie, cd install/test/mpi /home/apps/mpich2/bin/mpirun -np 4 ../../../bin/dock6.mpi -i mpi.dockin -o mpi.dockmpiout Scott > > Can you run other MPI programs ? > > > > Scott > > > > I run amber over lam-mpi. I'm not experienced with mpich2. Maybe I > might be doing something wrong! > > By this poor report, can you have any idea of what might be happening? > > Thanks a lot, one more time! > > > > make[1]: Entering directory `/home/apps/dock/dock6/install/test/mpi' > cd ../grid_generation && make test > make[2]: Entering directory `/home/apps/dock/dock6/install/test/grid_generation' > # Construct box to enclose spheres > ../../../bin/showbox < box.in > /dev/null > ../dockdif box.pdb.save box.pdb > diffing box.pdb.save with box.pdb > PASSED > ============================================================== > # Compute scoring grids > ../../../bin/grid -i grid.in -o grid.out > ../dockdif grid.out.save grid.out > diffing grid.out.save with grid.out > PASSED > ============================================================== > make[2]: Leaving directory `/home/apps/dock/dock6/install/test/grid_generation' > make[1]: Leaving directory `/home/apps/dock/dock6/install/test/mpi' > make[1]: Entering directory `/home/apps/dock/dock6/install/test/mpi' > > Processing test mpi > /home/apps/mpich2/bin/mpirun -np 2 ../../../bin/dock6.mpi -i > mpi.dockin -o mpi.dockmpiout > Initializing MPI Routines... > Initializing MPI Routines... > ../dockdif -t 8 mpi.dockmpiout.save mpi.dockmpiout > diffing mpi.dockmpiout.save with mpi.dockmpiout > possible FAILURE: check mpi.dockmpiout.dif > ============================================================== > diffing mpi_ranked.mol2.save with mpi_ranked.mol2 > possible FAILURE: check mpi_ranked.mol2.dif > ============================================================== > make[1]: Leaving directory `/home/apps/dock/dock6/install/test/mpi' > > > more mpi.dockmpiout.dif : > > > 106c106 > < Conformations: 3 > --- > > Conformations: 4 > 110a111,118 > > Molecule: ZINC01555236 > > Anchors: 1 > > Orientations: 50 > > Conformations: 18 > > Grid Score: 501606144. > > vdw: 501606144. > > es: -10. > > ----------------------------------- > 114,117c122,125 > < Conformations: 6 > < Grid Score: 21. > < vdw: 19. > < es: 1. > --- > > Conformations: 7 > > Grid Score: -12. > > vdw: -12. > > es: -0. > 123,125c131,133 > < Grid Score: 19. > < vdw: 20. > < es: -1. > --- > > Grid Score: 30. > > vdw: 32. > > es: -2. > 130,133c138,141 > < Conformations: 48 > < Grid Score: -15. > < vdw: -13. > < es: -1. > --- > > Conformations: 44 > > Grid Score: -12. > > vdw: -12. > > es: -0. > 138c146 > < Conformations: 12 > --- > > Conformations: 16 > 146,148c154,156 > < Conformations: 6 > < Grid Score: 145519. > < vdw: 145519. > --- > > Conformations: 2 > > Grid Score: 168506. > > vdw: 168506. > 154c162 > < Conformations: 28 > --- > > Conformations: 29 > From sbrozell at scripps.edu Tue Jul 10 13:23:35 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Tue, 10 Jul 2007 13:23:35 -0700 Subject: [Dock-fans] failure on dock.mpi In-Reply-To: <86ad38fa0707101251g1e7570dcw816f310f18fb5ee3@mail.gmail.com> References: <86ad38fa0707091016j29035fe8vf101460bfefd3ea7@mail.gmail.com> <86ad38fa0707091532u87eef91me6ffcef96e63d491@mail.gmail.com> <86ad38fa0707101251g1e7570dcw816f310f18fb5ee3@mail.gmail.com> Message-ID: Hi, On Tue, 10 Jul 2007, Alessandro Nascimento wrote: > using the same mpich implementation I compiled pmemd (software of > particle mesh ewald implementation in amber 9). It is running okay in > my cluster now on the 5 nodes (6 processors). > However, neither dock parallel tests or my own dock run there.... > Just to mention, my machines are Intel Xeon 64 (3.4Ghz), in a Gigabit > network (I don't know if hardware issue matter in this kind of > problems). > As was mentioned, it may be a mpi problem rather than dock problems. I > just would like to know if has anyone else seen the same problem.... > > Initializing MPI Routines... > Initializing MPI Routines... > Initializing MPI Routines... > Initializing MPI Routines... > tail -f rigid.out > cluster_rmsd_threshold 2.0 > num_clusterheads_for_rescore 5 > num_secondary_scored_conformers_written 4 > rank_primary_ligands no > rank_secondary_ligands no > > Initializing Library File Routines... > Initializing Orienting Routines... > Initializing Grid Score Routines... > Reading the energy grid from grid.nrg > [cli_1]: aborting job: One possibility is that your file system is not distributed across nodes; thus some processes may not be able to read the grid file. Have you done a distributed copy of all of the input files ? Have you examined the per process dock output files, ie, rigid.out.1, rigid.out.2, ... There may be more specific error messages in them. Scott > Fatal error in MPI_Recv: Other MPI error, error stack: > MPI_Recv(186).............................: > MPI_Recv(buf=0x7fffffc48f1c, count=2, MPI_INT, src=0, tag=100, > MPI_COMM_WORLD, status=0x7fffffc46620) failed > MPIDI_CH3_Progress_wait(212)..............: an error occurred while > handling an event returned by MPIDU_Sock_Wait() > MPIDI_CH3I_Progress_handle_sock_event(413): > MPIDU_Socki_handle_read(633)..............: connection failure > (set=0,sock=1,errno=104:Connection reset by peer) > rank 0 in job 6 ruska_34405 caused collective abort of all ranks > exit status of rank 0: killed by signal 11 > > ----------------------------------- > Molecule: ZINC00000012 > > Anchors: 1 > Orientations: 120000 > Conformations: 2375 > > Primary Score > [2] Exit 11 /home/apps/mpich2/bin/mpiexec -n 5 > /home/apps/dock/dock6/bin/dock6.mpi -i rigid.in -o rigid.out > NEWS! In-Reply-To: <86ad38fa0707101351v74c250edh7c828df008393a55@mail.gmail.com> References: <86ad38fa0707101351v74c250edh7c828df008393a55@mail.gmail.com> Message-ID: Hi, On Tue, 10 Jul 2007, Alessandro Nascimento wrote: > my files are distributed over RAID... however, I tried to reboot my > system and restart again. > The same error occurs. > > However, I noticed that if change the line in my input dock file: > > grid_score_secondary yes ==> no > > My docking runs well unitl the end in parallel. What exactly does that mean ? If you make this change > grid_score_secondary yes ==> no then with everything else the same dock.mpi completes successfully ? How does that output compare with the serial output ? Please send me your complete dock input file; I'll try to reproduce the failure. Scott > So, I might be experiencing some problem with this function when I run > dock in parallel. > Does this information helps you to figure out what might me happening? > > Best regards, > > > -alessandro > > > On 7/10/07, Scott Brozell wrote: > > Hi, > > > > On Tue, 10 Jul 2007, Alessandro Nascimento wrote: > > > > > using the same mpich implementation I compiled pmemd (software of > > > particle mesh ewald implementation in amber 9). It is running okay in > > > my cluster now on the 5 nodes (6 processors). > > > However, neither dock parallel tests or my own dock run there.... > > > Just to mention, my machines are Intel Xeon 64 (3.4Ghz), in a Gigabit > > > network (I don't know if hardware issue matter in this kind of > > > problems). > > > As was mentioned, it may be a mpi problem rather than dock problems. I > > > just would like to know if has anyone else seen the same problem.... > > > > > > Initializing MPI Routines... > > > Initializing MPI Routines... > > > Initializing MPI Routines... > > > Initializing MPI Routines... > > > tail -f rigid.out > > > cluster_rmsd_threshold 2.0 > > > num_clusterheads_for_rescore 5 > > > num_secondary_scored_conformers_written 4 > > > rank_primary_ligands no > > > rank_secondary_ligands no > > > > > > Initializing Library File Routines... > > > Initializing Orienting Routines... > > > Initializing Grid Score Routines... > > > Reading the energy grid from grid.nrg > > > [cli_1]: aborting job: > > > > One possibility is that your file system is not distributed > > across nodes; thus some processes may not be able to read > > the grid file. Have you done a distributed copy of all of the > > input files ? > > > > Have you examined the per process dock output files, ie, > > rigid.out.1, rigid.out.2, ... > > There may be more specific error messages in them. > > > > Scott > > > > > Fatal error in MPI_Recv: Other MPI error, error stack: > > > MPI_Recv(186).............................: > > > MPI_Recv(buf=0x7fffffc48f1c, count=2, MPI_INT, src=0, tag=100, > > > MPI_COMM_WORLD, status=0x7fffffc46620) failed > > > MPIDI_CH3_Progress_wait(212)..............: an error occurred while > > > handling an event returned by MPIDU_Sock_Wait() > > > MPIDI_CH3I_Progress_handle_sock_event(413): > > > MPIDU_Socki_handle_read(633)..............: connection failure > > > (set=0,sock=1,errno=104:Connection reset by peer) > > > rank 0 in job 6 ruska_34405 caused collective abort of all ranks > > > exit status of rank 0: killed by signal 11 > > > > > > ----------------------------------- > > > Molecule: ZINC00000012 > > > > > > Anchors: 1 > > > Orientations: 120000 > > > Conformations: 2375 > > > > > > Primary Score > > > [2] Exit 11 /home/apps/mpich2/bin/mpiexec -n 5 > > > /home/apps/dock/dock6/bin/dock6.mpi -i rigid.in -o rigid.out > > > NEWS! In-Reply-To: References: <86ad38fa0707101351v74c250edh7c828df008393a55@mail.gmail.com> Message-ID: <86ad38fa0707102002n5fb72bawdc21c2839f997e54@mail.gmail.com> Hi Scott, sorry if I was not clear. My guess is that there is something with secondary score in my docking. The input file I attached to this mail runs well in parallel on my cluster. However if I enable grid_score_secundary, I got the error with mpi. Also, the same happens with continuous_score_secondary. I didn't compare the results of parallel and serial jobs yet. I will take a look at them... I can put my receptor file and grid files in a ftp/http server if you want to reproduce exactly what I am doing. Best Regards, -alessandro On 7/10/07, Scott Brozell wrote: > Hi, > > On Tue, 10 Jul 2007, Alessandro Nascimento wrote: > > > my files are distributed over RAID... however, I tried to reboot my > > system and restart again. > > The same error occurs. > > > > However, I noticed that if change the line in my input dock file: > > > > grid_score_secondary yes ==> no > > > > My docking runs well unitl the end in parallel. > > What exactly does that mean ? > If you make this change > > grid_score_secondary yes ==> no > then with everything else the same dock.mpi completes successfully ? > How does that output compare with the serial output ? > Please send me your complete dock input file; > I'll try to reproduce the failure. > > Scott > > > So, I might be experiencing some problem with this function when I run > > dock in parallel. > > Does this information helps you to figure out what might me happening? > > > > Best regards, > > > > > > -alessandro > > > > > > On 7/10/07, Scott Brozell wrote: > > > Hi, > > > > > > On Tue, 10 Jul 2007, Alessandro Nascimento wrote: > > > > > > > using the same mpich implementation I compiled pmemd (software of > > > > particle mesh ewald implementation in amber 9). It is running okay in > > > > my cluster now on the 5 nodes (6 processors). > > > > However, neither dock parallel tests or my own dock run there.... > > > > Just to mention, my machines are Intel Xeon 64 (3.4Ghz), in a Gigabit > > > > network (I don't know if hardware issue matter in this kind of > > > > problems). > > > > As was mentioned, it may be a mpi problem rather than dock problems. I > > > > just would like to know if has anyone else seen the same problem.... > > > > > > > > Initializing MPI Routines... > > > > Initializing MPI Routines... > > > > Initializing MPI Routines... > > > > Initializing MPI Routines... > > > > tail -f rigid.out > > > > cluster_rmsd_threshold 2.0 > > > > num_clusterheads_for_rescore 5 > > > > num_secondary_scored_conformers_written 4 > > > > rank_primary_ligands no > > > > rank_secondary_ligands no > > > > > > > > Initializing Library File Routines... > > > > Initializing Orienting Routines... > > > > Initializing Grid Score Routines... > > > > Reading the energy grid from grid.nrg > > > > [cli_1]: aborting job: > > > > > > One possibility is that your file system is not distributed > > > across nodes; thus some processes may not be able to read > > > the grid file. Have you done a distributed copy of all of the > > > input files ? > > > > > > Have you examined the per process dock output files, ie, > > > rigid.out.1, rigid.out.2, ... > > > There may be more specific error messages in them. > > > > > > Scott > > > > > > > Fatal error in MPI_Recv: Other MPI error, error stack: > > > > MPI_Recv(186).............................: > > > > MPI_Recv(buf=0x7fffffc48f1c, count=2, MPI_INT, src=0, tag=100, > > > > MPI_COMM_WORLD, status=0x7fffffc46620) failed > > > > MPIDI_CH3_Progress_wait(212)..............: an error occurred while > > > > handling an event returned by MPIDU_Sock_Wait() > > > > MPIDI_CH3I_Progress_handle_sock_event(413): > > > > MPIDU_Socki_handle_read(633)..............: connection failure > > > > (set=0,sock=1,errno=104:Connection reset by peer) > > > > rank 0 in job 6 ruska_34405 caused collective abort of all ranks > > > > exit status of rank 0: killed by signal 11 > > > > > > > > ----------------------------------- > > > > Molecule: ZINC00000012 > > > > > > > > Anchors: 1 > > > > Orientations: 120000 > > > > Conformations: 2375 > > > > > > > > Primary Score > > > > [2] Exit 11 /home/apps/mpich2/bin/mpiexec -n 5 > > > > /home/apps/dock/dock6/bin/dock6.mpi -i rigid.in -o rigid.out > > > > -- [ ]s --alessandro -------------- next part -------------- A non-text attachment was scrubbed... Name: rigid.in Type: application/octet-stream Size: 4163 bytes Desc: not available Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070711/44d5e571/attachment.obj From mikesilb at bnl.gov Wed Jul 11 06:26:41 2007 From: mikesilb at bnl.gov (Silberstein, Michael) Date: Wed, 11 Jul 2007 09:26:41 -0400 Subject: [Dock-fans] Error messages when docking specific molecules within ZINC-derived library Message-ID: Hi, I am a novice at docking larger libraries, and so, the following inquiry represents some of my current difficulties in docking (using DOCK 4.0.1) a ZINC-database derived mini-library. I have attempted to dock a library of ~3000 compounds to various zinc-metalloproteases. Even though 3000 separate molecules were included (in one large .mol2 file), only ~ 600 of them were able to provide docking results. The remaining 2400 compounds gave the following error: WARNING read_mol2: Error reading ATOM record for ZINC00001648 in ./xyz.mol2. WARNING read_mol2: Error reading ATOM record for ZINC00001825 in ./xyz.mol2. WARNING read_mol2: Improper BOND origin/target for ZINC00001932 in ./xyz.mol2. WARNING read_mol2: Error reading ATOM record for ZINC00002585 in ./xyz.mol2. WARNING read_mol2: Error reading ATOM record for ZINC00002588 in ./xyz.mol2. WARNING read_mol2: Error reading ATOM record for ZINC00002819 in ./xyz.mol2. WARNING read_mol2: Improper BOND origin/target for ZINC00003421 in ./xyz.mol2. and so on... Can anyone explain to me what might be wrong with the format of these individual .mol2 files such that either the ATOMs or BONDs cannot be read-in properly in order to have these molecules docked?? Since this analysis has been already performed using DOCK 4.0, it would be really good if I would not have to potentially repeat this using a newer version of DOCK. So it would be preferable if any suggestions/comments be regarding (specifically) DOCK 4.0 and why the program is having trouble reading in such a large percentage of ZINC database-derived .mol2 files. Any suggestion would be very helpful at this point. Thanks in advance. Sincerely, Mike Silberstein From mikesilb at bnl.gov Wed Jul 11 07:16:59 2007 From: mikesilb at bnl.gov (Silberstein, Michael) Date: Wed, 11 Jul 2007 10:16:59 -0400 Subject: [Dock-fans] Further analysis of the error messages when docking ZINC-derived library Message-ID: Hi again, This post is highly related to the last post that I made "Error messages when docking specific molecules withinZINC-derived library" and has more detail as to my current difficulties. In the last post, I mentioned that many compounds in my ZINC database-derived library had errors of the form WARNING read_mol2: Error reading ATOM record for ZINC00002585 in ./xyz.mol2. WARNING read_mol2: Error reading ATOM record for ZINC00002588 in ./xyz.mol2. WARNING read_mol2: Error reading ATOM record for ZINC00002819 in ./xyz.mol2. WARNING read_mol2: Improper BOND origin/target for ZINC00003421 in ./xyz.mol2. and so on... ------------------------------------------------------------------------------------------ In this post, I will describe some highly odd results pertaining to one particular molecule that has been giving me the above error message. For one of the compounds in my mini-library, ZINC00014272, I received the above error message, and started further investigating why this particular molecule was not working. This molecule apparently has three separate .mol2 files. (By the way, what dictates whether a given molecule might have multiple .mol2, SDF, SMILES (etc.) file formats?? Various protonation states? Different conformers? Or simply, different programs that generate various .mol2 outputs? Why would ZINC00014272 contain three sub-entries?) Using these three different .mol2 files, I noticed that in my mini-library docking output (using DOCK 4.0.1), only the 2nd of the three molecules provided docking output (i.e. molecules #1 and #3 provided the above error message). I was curious as to why only #2 worked while #1 and #3 failed, so I started docking each of them individually and afterwards, in various combinations. I received highly odd results. The following represents the results that I got. Maybe one of you can make some sense of it: 1. Prior 3000 member library docking - #2 docked followed by an error message (presumably from molecule #3) 2. Docked only #1 - Docking failed and program crashed (mutilple computer address symbols showed up in the DOCK results. If you want further clarification as to this 'crashed output', I can show it to you in a subsequent post.) 3. Docked only #2 - Docking failed and program crashed. (I found this to be surprising since in my larger library, #2 was the only one that docked normally.) 4. Docked only #3 - Docking failed and program crashed. 5. Docked #1 followed by #2 - #2 docked fine, although #1 had no error message whatsoever. There were no error messages at all in the output. 6. Docked #1 followed by #3 - Docking failed and program crashed 7. Docked #2 followed by #3 - Docking failed and program crashed (Again, I found this quite surprising.) One error message was found in output. (My guess is that this is from #3) 8. Docked #2 followed by #1 - Docking failed and program crashed 9. Docked #1 followed by #2 followed by #3 - Exact same results as seen when docking the 3000-membered library. Only #2 docked properly, while #3 (presumably) gave the error message. 10. ZINC00012908 followed by #1 followed by #2 followed by #3 followed by ZINC00015788 - Same results as seen in scenario 9 (and scenario 1). However surprisingly, the two flanking molecules ZINC00012908 and ZINC00015788 had no noticeable output whatsoever, and was clearly not docked at all. It was as if these two molecules did not exist in the input .mol2 file at all. So these are my results, and I find myself incredibly confused as to why only #2 worked, why it had to work only following #1, and why the additional (flanking) compounds were not even found within the DOCK output and were certainly not docked. Again, this analysis was all performed using DOCK 4.0.1 . Perhaps switching to a newer version of DOCK might help too. However, I have already analyzed much of the results (the molecules that DID dock properly), and would rather focus on what I have, rather than to install the newer DOCK version. I would again appreciate any comments, focusing on the DOCK 4 output, rather than simply shifting immediately to DOCK 5 and/or 6. If anyone can provide any insight as to these highly peculiar results, I would absolutely appreciate it. Thank you very much in advance. Sincerely, Mike Silberstein From mabdu3 at email.uky.edu Wed Jul 11 09:16:00 2007 From: mabdu3 at email.uky.edu (Abdul Hameed, MohamedDiwanMo) Date: Wed, 11 Jul 2007 12:16:00 -0400 Subject: [Dock-fans] min anchor size -query Message-ID: <62D3F106CB16C34D825A1B75EFBA6839D5929156@EX7FM04.ad.uky.edu> Hello all, I am trying target a small sub-pocket in a protein. Will it be useful to reduce the "min_anchor_size" parameter to 6 in that case? The default value is given as 40. I am also curious to know whether changing this parameter will have any big impact on the results. Your comments will be very helpful. Thanks and Regards, Mohamed Diwan Graduate student, University of Kentucky. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070711/bfb929ad/attachment.html From JShultz at nas.edu Wed Jul 11 12:32:35 2007 From: JShultz at nas.edu (Shultz, Jack) Date: Wed, 11 Jul 2007 15:32:35 -0400 Subject: [Dock-fans] BOINC Platform Message-ID: Does Dock 6 have support for BOINC API libraries? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070711/3ad286d4/attachment.html From sbrozell at scripps.edu Wed Jul 11 19:51:19 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Wed, 11 Jul 2007 19:51:19 -0700 Subject: [Dock-fans] BOINC Platform In-Reply-To: References: Message-ID: Hi, 6 does not support bionic api's. millions of api's could have been supported. dollars do not exist for that, however. man kind should do more docking, but so many are cyborgs. On Wed, 11 Jul 2007, Shultz, Jack wrote: > Does Dock 6 have support for BOINC API libraries? http://boinc.berkeley.edu/ Interesting work; we have heard of seti, einstein, and folding at home. Steve Austin Jamie Sommers http://en.wikipedia.org/wiki/Bionic_Woman_%282007_TV_series%29 :) From sudmukh at yahoo.com Wed Jul 11 20:55:21 2007 From: sudmukh at yahoo.com (Sudipto Mukherjee) Date: Wed, 11 Jul 2007 20:55:21 -0700 (PDT) Subject: [Dock-fans] min anchor size -query Message-ID: <732492.44972.qm@web36710.mail.mud.yahoo.com> Mohamed, The min_anchor_size is the minimum number of atoms used for the anchor. The value of 40 is artificially high. This makes dock use the largest rigid segment of the ligand as the anchor. If you want dock to consider more than one possible anchor, you can reduce this to a smaller size. '6' would likely pick benzene rings as the anchor. However, note that the full anchor and grow procedure is performed for each anchor. This might make docking run much slower, and yield a lot of similar poses. 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: "Abdul Hameed, MohamedDiwanMo" To: "dock-fans at docking.org" Sent: Wednesday, July 11, 2007 12:16:00 PM Subject: [Dock-fans] min anchor size -query Hello all, I am trying target a small sub-pocket in a protein. Will it be useful to reduce the ?min_anchor_size? parameter to 6 in that case? The default value is given as 40. I am also curious to know whether changing this parameter will have any big impact on the results. Your comments will be very helpful. Thanks and Regards, Mohamed Diwan Graduate student, University of Kentucky. _______________________________________________ Dock-fans mailing list Dock-fans at docking.org http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans Got a little couch potato? Check out fun summer activities for kids. ____________________________________________________________________________________ Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070711/43af5323/attachment.html From rafi4dd at gmail.com Fri Jul 13 06:20:54 2007 From: rafi4dd at gmail.com (rafi A) Date: Fri, 13 Jul 2007 09:20:54 -0400 Subject: [Dock-fans] secondary scoring function Message-ID: <2bdc62b30707130620q2772a4b1g373fe074c60e3978@mail.gmail.com> Hello, I am a new user of DOCK and i am having some basic questions. I am interested to know about the secondary scoring function used for DOCK. Particularly what is the secondary scoring function used frequently (or found to be more useful)?. >From the manual I understand that sec. scoring function is used in the final minimization, scoring and ranking of molecules. I tried using grid scoring for both primary and secondary scoring function. But the results in the ranked files for primary and secondary scoring function are both same. In this case should I attempt docking without using any secondary scoring function.( rank_secondary_ligands: no). Thanks in advance. Best Regards, Rafi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070713/c70a2dd6/attachment-0001.html From loraine.brillet at cea.fr Mon Jul 16 00:18:39 2007 From: loraine.brillet at cea.fr (BRILLET Loraine 216515) Date: Mon, 16 Jul 2007 09:18:39 +0200 Subject: [Dock-fans] ligand file input Message-ID: <7E82589CA662294BB063FBCD85928FF9888027@TOKYO.intra.cea.fr> Dear all, I have noticed that the Tripos mol2 atom/bond types given to ligands when converting them to mol2 format depend on the program used to do that. For example, I used Chimera and OpenBabel to prepare the mol2 file for nocodazole (adding H and partial charges). You can see that the atom/bond types are different (see files included). Do these different atom/bond types have an influence on the docking results with DOCK? Regards, Loraine Brillet -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070716/8f978deb/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: nocodazole_chimera.mol2 Type: application/octet-stream Size: 3334 bytes Desc: nocodazole_chimera.mol2 Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070716/8f978deb/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: nocodazole_openbabel.mol2 Type: application/octet-stream Size: 3373 bytes Desc: nocodazole_openbabel.mol2 Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070716/8f978deb/attachment-0001.obj From jji at cgl.ucsf.edu Mon Jul 16 10:29:50 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Mon, 16 Jul 2007 10:29:50 -0700 Subject: [Dock-fans] ligand file input In-Reply-To: <7E82589CA662294BB063FBCD85928FF9888027@TOKYO.intra.cea.fr> References: <7E82589CA662294BB063FBCD85928FF9888027@TOKYO.intra.cea.fr> Message-ID: <469BAB0E.5070402@cgl.ucsf.edu> Hi Loraine As a general rule, if the atom type changes enough to give it a new AMBER atom type (e.g. C sp2 changes to C sp3) then DOCK results may be different due to different VDW parameters. Specifically, you have a bigger problem, as the first "C1" seems to be hexavalent. and the second "C1" seems to be pentavalent. There is also a hexavalent N. We recommend OEChem from OpenEye for converting file formats. Good luck! John BRILLET Loraine 216515 wrote: > > Dear all, > > > > I have noticed that the Tripos mol2 atom/bond types given to ligands > when converting them to mol2 format depend on the program used to do > that. For example, I used Chimera and OpenBabel to prepare the mol2 > file for nocodazole (adding H and partial charges). You can see that > the atom/bond types are different (see files included). > > Do these different atom/bond types have an influence on the docking > results with DOCK? > > > > Regards, > > > > Loraine Brillet > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > From pett at cgl.ucsf.edu Mon Jul 16 17:27:18 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 16 Jul 2007 17:27:18 -0700 Subject: [Dock-fans] ligand file input Message-ID: What I can say is that all the discrepancies favor the OpenBabel version, so you should use that. I will work on making Chimera perform better here. The discrepancies I can see are: 1) wrong bond orders between aromatic carbons and non-ring sp2 heavy atoms 2) failure to identify amide moiety 3) failure to use N.ar type for aromatic ring nitrogens --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070716/a95bb697/attachment.html From jji at cgl.ucsf.edu Fri Jul 20 16:37:15 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Fri, 20 Jul 2007 16:37:15 -0700 Subject: [Dock-fans] Error messages when docking specific molecules within ZINC-derived library In-Reply-To: References: Message-ID: <46A1472B.8040605@cgl.ucsf.edu> Hi Mike If you are using DOCK 4, are you adding the "substructure" record to the end of each mol2 entry as required? Two methods are referenced on the ZINC home page: http://blaster.docking.org/zinc/fix_substructure.py http://blaster.docking.org/zinc/zinc_convert.csh.txt If you are doing this already, please let me know and we will go on to the next step. Good luck! John Silberstein, Michael wrote: > Hi, > > I am a novice at docking larger libraries, and so, the following inquiry represents some of my current difficulties in docking (using DOCK 4.0.1) a ZINC-database derived mini-library. > > I have attempted to dock a library of ~3000 compounds to various zinc-metalloproteases. Even though 3000 separate molecules were included (in one large .mol2 file), only ~ 600 of them were able to provide docking results. The remaining 2400 compounds gave the following error: > > WARNING read_mol2: Error reading ATOM record for ZINC00001648 in ./xyz.mol2. > WARNING read_mol2: Error reading ATOM record for ZINC00001825 in ./xyz.mol2. > WARNING read_mol2: Improper BOND origin/target for ZINC00001932 in ./xyz.mol2. > WARNING read_mol2: Error reading ATOM record for ZINC00002585 in ./xyz.mol2. > WARNING read_mol2: Error reading ATOM record for ZINC00002588 in ./xyz.mol2. > WARNING read_mol2: Error reading ATOM record for ZINC00002819 in ./xyz.mol2. > WARNING read_mol2: Improper BOND origin/target for ZINC00003421 in ./xyz.mol2. > > and so on... > > Can anyone explain to me what might be wrong with the format of these individual .mol2 files such that either the ATOMs or BONDs cannot be read-in properly in order to have these molecules docked?? > > Since this analysis has been already performed using DOCK 4.0, it would be really good if I would not have to potentially repeat this using a newer version of DOCK. So it would be preferable if any suggestions/comments be regarding (specifically) DOCK 4.0 and why the program is having trouble reading in such a large percentage of ZINC database-derived .mol2 files. Any suggestion would be very helpful at this point. Thanks in advance. > > > Sincerely, > Mike Silberstein > > > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > From pkmankoo at gmail.com Tue Jul 24 16:08:22 2007 From: pkmankoo at gmail.com (Parminder Mankoo) Date: Tue, 24 Jul 2007 19:08:22 -0400 Subject: [Dock-fans] problem with dms: Message-ID: <2a88b09d0707241608he2866fbg1e7e36851b30d0ae@mail.gmail.com> Hello, I am trying to learn DOCK6 to dock atp into a kinase. I am following the tutorials and now stuck at the step where I need _____________________ ../dms/bin/dms atp.pdb -n -w 1.4 -v -o atp.ms No atoms in input file! ________________________ The atp.pdb file is not empty. It is as following: I will appreciate any help. Thanks, preeti EXPDTA THEORETICAL MODEL, MODELLER SVN 2007/07/16 21:23:51 ATOM 1 PG ATP 1391 28.876 68.006 19.624 1.00 92.35 P ATOM 2 O3B ATP 1391 27.839 66.717 19.158 1.00 91.75 O ATOM 3 PB ATP 1391 27.136 66.147 17.708 1.00 89.86 P ATOM 4 O3A ATP 1391 25.700 65.646 18.125 1.00 89.34 O ATOM 5 PA ATP 1391 24.999 64.238 18.558 1.00 88.85 P ATOM 6 O5' ATP 1391 23.527 64.665 18.713 1.00 86.03 O ATOM 7 C5' ATP 1391 23.084 65.460 19.796 1.00 84.42 C ATOM 8 C4' ATP 1391 21.636 65.673 19.598 1.00 80.99 C ATOM 9 C3' ATP 1391 20.999 66.481 20.692 1.00 80.39 C ATOM 10 C2' ATP 1391 20.210 65.462 21.489 1.00 78.56 C ATOM 11 C1' ATP 1391 20.120 64.139 20.656 1.00 76.25 C ATOM 12 N9 ATP 1391 20.605 62.931 21.426 1.00 72.25 N ATOM 13 C4 ATP 1391 19.867 62.159 22.282 1.00 69.34 C ATOM 14 N3 ATP 1391 18.539 62.305 22.599 1.00 67.00 N ATOM 15 C2 ATP 1391 18.146 61.357 23.483 1.00 66.09 C ATOM 16 N1 ATP 1391 18.880 60.379 24.016 1.00 66.25 N ATOM 17 C6 ATP 1391 20.194 60.265 23.667 1.00 67.23 C ATOM 18 N6 ATP 1391 20.953 59.309 24.176 1.00 66.15 N ATOM 19 C5 ATP 1391 20.737 61.194 22.759 1.00 69.38 C ATOM 20 N7 ATP 1391 22.010 61.321 22.230 1.00 70.26 N ATOM 21 C8 ATP 1391 21.872 62.362 21.456 1.00 70.59 C ATOM 22 O4' ATP 1391 21.008 64.371 19.546 1.00 79.07 O ATOM 23 O2' ATP 1391 18.893 65.918 21.763 1.00 79.22 O ATOM 24 O3' ATP 1391 20.174 67.484 20.024 1.00 83.82 O ATOM 25 O2A ATP 1391 25.487 63.690 19.829 1.00 86.17 O ATOM 26 O1A ATP 1391 25.072 63.410 17.343 1.00 90.83 O ATOM 27 O2B ATP 1391 27.063 67.238 16.699 1.00 92.00 O ATOM 28 O1B ATP 1391 27.841 64.910 17.278 1.00 89.89 O ATOM 29 O3G ATP 1391 28.367 68.556 20.926 1.00 91.62 O ATOM 30 O2G ATP 1391 30.180 67.348 19.772 1.00 93.97 O ATOM 31 O1G ATP 1391 28.827 69.027 18.566 1.00 93.43 O END -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070724/44df10b7/attachment-0001.html From al.s.nascimento at gmail.com Wed Jul 25 17:46:05 2007 From: al.s.nascimento at gmail.com (Alessandro Nascimento) Date: Wed, 25 Jul 2007 21:46:05 -0300 Subject: [Dock-fans] Amber scoring Message-ID: <86ad38fa0707251746m602e9d37g2d8668e9d90b8047@mail.gmail.com> Hi Dock-fans I would like to know from those who have already achieved good results using grid (primary) / amber (secondary) score to search databases like zinc: is there any good threshold to be used as an indicative of success by amber scoring function? In dock6 tutorial page there's a graph showing binders and decoys using amber score. There, the best binder achieves ~ -17.00 as amber score. Would this value be a good indicative? Regards -- [ ]s --alessandro From lucioric at ibt.unam.mx Wed Jul 25 18:10:14 2007 From: lucioric at ibt.unam.mx (lucioric at ibt.unam.mx) Date: Wed, 25 Jul 2007 20:10:14 -0500 Subject: [Dock-fans] Unsuscribe Message-ID: <1185412214.46a7f47629fdd@webmail.ibt.unam.mx> I want to unsuscribe fron this mailing list. Sincerely yours. Lucio. ---------------------------------------------------------------- Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. From keshet1 at umbc.edu Thu Jul 26 10:51:37 2007 From: keshet1 at umbc.edu (Ben Keshet) Date: Thu, 26 Jul 2007 13:51:37 -0400 Subject: [Dock-fans] positive score in Amber In-Reply-To: Message-ID: <004d01c7cfad$9d2c3380$29ad5582@umbc80a173302c> Hi Dock-fans, I am using Amber score to dock the Grid score results. However, I keep getting positive scores for all of my Amber runs and trying to understand why: 1. Does anyone know if the 4 steps of Amber (minimization, MD simulation, minimization, energy evaluation) are running once, or repeating until some parameter is reaching some value? 2. What does the parameter amber_score_nonbonded_cutoff means? Does 'nonbonded' means non-bonded to the ligand or to the receptor? In other words, if my receptor is bigger than the amber_score_nonbonded_cutoff, some of it is not be included in the energy calculation? 3. Can anyone give me some hints on how to read the verbose OUT file to see whether I should increase the minimization steps or the MD steps? Thank you for your help, Ben From sbrozell at scripps.edu Thu Jul 26 12:51:30 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Thu, 26 Jul 2007 12:51:30 -0700 Subject: [Dock-fans] positive score in Amber In-Reply-To: <004d01c7cfad$9d2c3380$29ad5582@umbc80a173302c> References: <004d01c7cfad$9d2c3380$29ad5582@umbc80a173302c> Message-ID: Hi, On Thu, 26 Jul 2007, Ben Keshet wrote: > I am using Amber score to dock the Grid score results. However, I keep > getting positive scores for all of my Amber runs and trying to understand > why: See my previous posts on errors in docking: http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-July/001103.html > 1. Does anyone know if the 4 steps of Amber (minimization, MD simulation, > minimization, energy evaluation) are running once, or repeating until some > parameter is reaching some value? In general, see the fourth paragraph in this section of the manual: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore In particular, both minimizations will proceed until their maximum number of cycles have been performed (amber_score_before_md_minimization_cycles and amber_score_after_md_minimization_cycles), or until the root-mean- square of the components of the gradient are less than 0.1. (In Dock 6.2 0.1 will be an adjustable input parameter.) > 2. What does the parameter amber_score_nonbonded_cutoff means? Does > 'nonbonded' means non-bonded to the ligand or to the receptor? In other > words, if my receptor is bigger than the amber_score_nonbonded_cutoff, some > of it is not be included in the energy calculation? In general, see that parameter description in this section of the manual: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore In particular, this cutoff is used to truncate the list of nonbonded pairs (on an atom-by-atom basis) in every GB calculation. See page 101 of the Amber 9 manual http://amber.scripps.edu/doc9/index.html Your second and third questions indicate that you do not understand the basics of molecular dynamics. Read section 1.1 of the Amber9 manual for a description of useful texts. The answer to the 2nd question is non-bonded over the set of all atoms. The answer to the 3rd question is no in the sense that you probably mean. > 3. Can anyone give me some hints on how to read the verbose OUT file to see > whether I should increase the minimization steps or the MD steps? In general, see the fourth last and the last paragraphs in this section of the manual: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore In particular, for the minimizations plot the energy per step and the rmsgrad per step. Likewise for the MD look for suspicious values and plot energy per step. Amber score is not black box software. Scott From sbrozell at scripps.edu Thu Jul 26 12:56:19 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Thu, 26 Jul 2007 12:56:19 -0700 Subject: [Dock-fans] Amber scoring In-Reply-To: <86ad38fa0707251746m602e9d37g2d8668e9d90b8047@mail.gmail.com> References: <86ad38fa0707251746m602e9d37g2d8668e9d90b8047@mail.gmail.com> Message-ID: Hi, On Wed, 25 Jul 2007, Alessandro Nascimento wrote: > I would like to know from those who have already achieved good results > using grid (primary) / amber (secondary) score to search databases > like zinc: is there any good threshold to be used as an indicative of > success by amber scoring function? I would also like to hear answers to this and not just for Amber score. In my limited experience its all relative. Here is my usual reference to the errors in docking http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-July/001103.html Scott > In dock6 tutorial page there's a graph showing binders and decoys > using amber score. There, the best binder achieves ~ -17.00 as amber > score. Would this value be a good indicative? From sbrozell at scripps.edu Thu Jul 26 15:13:45 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Thu, 26 Jul 2007 15:13:45 -0700 Subject: [Dock-fans] problem with dms: In-Reply-To: <2a88b09d0707241608he2866fbg1e7e36851b30d0ae@mail.gmail.com> References: <2a88b09d0707241608he2866fbg1e7e36851b30d0ae@mail.gmail.com> Message-ID: Hi, On Tue, 24 Jul 2007, Parminder Mankoo wrote: > I am trying to learn DOCK6 to dock atp into a kinase. I am following the > tutorials and now stuck at the step where I need > _____________________ > ../dms/bin/dms atp.pdb -n -w 1.4 -v -o atp.ms > > No atoms in input file! > ________________________ > > The atp.pdb file is not empty. It is as following: > EXPDTA THEORETICAL MODEL, MODELLER SVN 2007/07/16 21:23:51 > ATOM 1 PG ATP 1391 28.876 68.006 19.624 1.00 92.35 > P > ATOM 2 O3B ATP 1391 27.839 66.717 19.158 1.00 91.75 > O ... dms/man/man1/dms.1 -a Include all atoms, not just those in amino acid and nucleic acid residues. Also be careful with the PDB format http://www.wwpdb.org/documentation/format23/sect9.html EXPDTA THEORETICAL MODEL, MODELLER SVN 2007/07/16 21:23:51 12345678901234567890123456789012345678901234567890123456789012345678901234567890 ATOM 1 PG ATP 1391 28.876 68.006 19.624 1.00 92.35 P ATOM 2 O3B ATP 1391 27.839 66.717 19.158 1.00 91.75 O ATOM 3 PB ATP 1391 27.136 66.147 17.708 1.00 89.86 P ATOM 4 O3A ATP 1391 25.700 65.646 18.125 1.00 89.34 O ATOM 5 PA ATP 1391 24.999 64.238 18.558 1.00 88.85 P ATOM 6 O5' ATP 1391 23.527 64.665 18.713 1.00 86.03 O ATOM 7 C5' ATP 1391 23.084 65.460 19.796 1.00 84.42 C ATOM 8 C4' ATP 1391 21.636 65.673 19.598 1.00 80.99 C ../dms/bin/dms atp.pdb -a -n -w 1.4 -v -o atp.ms 8 atoms P 3 O 3 C 2 Servers initialized Neighbors computed Probes computed Neighbors sent Surface computed Server request count: localhost 79 862 points (569 contact, 293 reentrant) 161.65 sq. A (112.40 contact, 49.25 reentrant) 5.33 pts/sq.A (5.06 contact, 5.95 reentrant) Scott From andreyvoronkov at yandex.ru Fri Jul 27 02:44:19 2007 From: andreyvoronkov at yandex.ru (Voronkov Andrew) Date: Fri, 27 Jul 2007 13:44:19 +0400 Subject: [Dock-fans] mpirun problem Message-ID: <103191185529459@webmail18.yandex.ru> Dear Dock administration, how can I solve this problem? I've prepared this machinefile under Linux but still have the problems. PS I haven't found the answer in archives. Sincerely yours, Andrew [voronkov at qsar21 Flexible]$ mpirun -machinefile machinefile -np 6 /data/soft/dock5/bin/dock5mpi -i anchor_and_grow.in -o anchor_and_grow.out Cannot read machinefile. Looked for files with extension LINUX in directory /usr/local/mpich-pgi/share . -------- ?????????? ????????????? ????????? -------- -- ??? ????? ????????? ???????? ???. http://moikrug.ru/l -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: machinefile.txt Url: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070727/78fa0e46/attachment.txt From sbrozell at scripps.edu Fri Jul 27 09:32:19 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Fri, 27 Jul 2007 09:32:19 -0700 Subject: [Dock-fans] mpirun problem In-Reply-To: <103191185529459@webmail18.yandex.ru> References: <103191185529459@webmail18.yandex.ru> Message-ID: Hi, On Fri, 27 Jul 2007, Voronkov Andrew wrote: > how can I solve this problem? > I've prepared this machinefile under Linux but still have the problems. > > PS I haven't found the answer in archives. > > [voronkov at qsar21 Flexible]$ mpirun -machinefile machinefile -np 6 /data/soft/dock5/bin/dock5mpi -i anchor_and_grow.in -o anchor_and_grow.out > Cannot read machinefile. > Looked for files with extension LINUX in > directory /usr/local/mpich-pgi/share . First, I recommend that you upgrade to Dock 6.1. Second, this looks like a system administration problem - contact them. What is in /usr/local/mpich-pgi/share ? Does this exist: /usr/local/mpich-pgi/share/machinefile ? Does this exist: /usr/local/mpich-pgi/share/machinefile.LINUX ? Where is your machine file ? Sometimes it needs to be in one's home directory or in a filesystem that is mounted on all nodes. What happens with mpirun -np 1 /data/... ? Can you rsh between nodes ? Good luck, Scott From szhong at rx.umaryland.edu Sun Jul 29 19:33:48 2007 From: szhong at rx.umaryland.edu (Zhong, Shijun) Date: Sun, 29 Jul 2007 22:33:48 -0400 Subject: [Dock-fans] Dock-fans Digest, DOCK4 paper References: Message-ID: <99ACB209EDC58343B189A58BBA1B55FA0E68B9@cits-exch1.campus.umaryland.edu> Hi, Could you send me a PDF file of the DOCK4 paper? Ewing, T. J.; Makino, S.; Skillman, A. G.; Kuntz, I. D., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J. Comput. Aided Mol. Des. 2001, 15, 411-428 Thanks a lot! Shijun -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 3650 bytes Desc: not available Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070729/79fe03a2/attachment-0001.bin From biobrain at gmail.com Mon Jul 30 03:04:52 2007 From: biobrain at gmail.com (Imtiaz M.) Date: Mon, 30 Jul 2007 11:04:52 +0100 Subject: [Dock-fans] while running sphgen,?????? Message-ID: <59840f5f0707300304h132cab97ib393c77c45a2cfff@mail.gmail.com> Dear All , while running sphgen, I am getting following message imtiaz at linux-q01x:~/dock_test> sphgen fmt: end of file apparent state: unit 5 named INSPH last format: (A80) lately reading sequential formatted external IO Aborted What that mean and how i can proceed further From sbrozell at scripps.edu Mon Jul 30 10:00:36 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Mon, 30 Jul 2007 10:00:36 -0700 Subject: [Dock-fans] Dock-fans Digest, DOCK4 paper In-Reply-To: <99ACB209EDC58343B189A58BBA1B55FA0E68B9@cits-exch1.campus.umaryland.edu> References: <99ACB209EDC58343B189A58BBA1B55FA0E68B9@cits-exch1.campus.umaryland.edu> Message-ID: Hi, On Sun, 29 Jul 2007, Zhong, Shijun wrote: > Could you send me a PDF file of the DOCK4 paper? In general, NO. http://en.wikipedia.org/wiki/Copyright If your university's library does not subscribe to this journal then use interlibrary loan. > Ewing, T. J.; Makino, S.; Skillman, A. G.; Kuntz, I. D., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J. Comput. Aided Mol. Des. 2001, 15, 411-428 > J. Comput. Aided Mol. Des. is a Springer publication. Here is their copyright transfer agreement. http://64.233.169.104/search?q=cache:okRq-l0M5OUJ:www.springer.com/cda/content/document/cda_downloaddocument/CTS_generell.pdf+springer+copyright+transfer&hl=en&ct=clnk&cd=1&gl=us&client=firefox-a The copyright to this article is transferred to Springer (respective to owner if other than Springer and for U.S. government employees: to the extent transferable) effective if and when the article is accepted for publication. The author warrants that his/her contribution is original and that he/she has full power to make this grant. The author signs for and accepts responsibility for releasing this material on behalf of any and all co-authors. The copyright transfer covers the exclusive right to reproduce and distribute the article, including reprints, translations, photographic reproductions, microform, electronic form (offline, online) or any other reproductions of similar nature. An author may self-archive an author-created version of his/her article on his/her own website and his/her institutions repository, including his/her final version; however he/ she may not use the publishers PDF version which is posted on www.springerlink.com. Furthermore, the author may only post his/her version provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springers website. The link must be accompanied by the following text: The original publication is available at www.springerlink.com. Scott From sbrozell at scripps.edu Mon Jul 30 10:28:45 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Mon, 30 Jul 2007 10:28:45 -0700 Subject: [Dock-fans] while running sphgen,?????? In-Reply-To: <59840f5f0707300304h132cab97ib393c77c45a2cfff@mail.gmail.com> References: <59840f5f0707300304h132cab97ib393c77c45a2cfff@mail.gmail.com> Message-ID: Hi, On Mon, 30 Jul 2007, Imtiaz M. wrote: > imtiaz at linux-q01x:~/dock_test> sphgen > fmt: end of file > apparent state: unit 5 named INSPH > last format: (A80) > lately reading sequential formatted external IO > Aborted > > What that mean and how i can proceed further Before posting go to http://dock.compbio.ucsf.edu/DOCK_6/index.htm Go to the text area labeled: Search DOCK-Fans: Enter some text from the error message, eg: lately reading sequential formatted external IO Behold the awesome power: http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-December/000845.html Scott