From cpsosa at msi.umn.edu Mon Jul 7 08:34:48 2008 From: cpsosa at msi.umn.edu (Carlos P Sosa) Date: Mon, 7 Jul 2008 10:34:48 -0500 (CDT) Subject: [Dock-fans] BUILD_FOR_RDSOL Message-ID: <8a6743ec1194d14464d6d32d7380b60e.squirrel@www.msi.umn.edu> Hello, I just built Dock 6.2 on a Linux on POWER5 system. I had to comment BUILD_FOR_RDSOL flags. Does anybody know what system or functionality this is? This is part of ... src/docktools/convgrids Thanks, gridrdsl.mk:#CPPFLAGS = -DBUILD_FOR_RDSOL gridrdsl.mk:#FPPFLAGS = -DBUILD_FOR_RDSOL gridrdsl.mk_orig:CPPFLAGS = -DBUILD_FOR_RDSOL gridrdsl.mk_orig:FPPFLAGS = -DBUILD_FOR_RDSOL io_grid.c:#ifdef BUILD_FOR_RDSOL io_grid.c:#ifdef BUILD_FOR_RDSOL io_grid.c:#ifdef BUILD_FOR_RDSOL io_grid.c:#ifdef BUILD_FOR_RDSOL io_grid.c:#ifdef BUILD_FOR_RDSOL io_gridf.F:#ifdef BUILD_FOR_RDSOL io_gridf.F:#ifdef BUILD_FOR_RDSOL io_gridf.F:#ifdef BUILD_FOR_RDSOL score.h:#ifdef BUILD_FOR_RDSOL From sbrozell at scripps.edu Mon Jul 7 15:10:33 2008 From: sbrozell at scripps.edu (Scott Brozell) Date: Mon, 7 Jul 2008 15:10:33 -0700 (PDT) Subject: [Dock-fans] BUILD_FOR_RDSOL In-Reply-To: <8a6743ec1194d14464d6d32d7380b60e.squirrel@www.msi.umn.edu> Message-ID: Hi, These are accessory programs for DOCK3.5 Score http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#ChemGridScore http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#docktools Scott On Mon, 7 Jul 2008, Carlos P Sosa wrote: > I just built Dock 6.2 on a Linux on POWER5 system. I had to comment > BUILD_FOR_RDSOL flags. Does anybody know what system or functionality > this is? This is part of ... src/docktools/convgrids > > Thanks, > > gridrdsl.mk:#CPPFLAGS = -DBUILD_FOR_RDSOL > gridrdsl.mk:#FPPFLAGS = -DBUILD_FOR_RDSOL > gridrdsl.mk_orig:CPPFLAGS = -DBUILD_FOR_RDSOL > gridrdsl.mk_orig:FPPFLAGS = -DBUILD_FOR_RDSOL > io_grid.c:#ifdef BUILD_FOR_RDSOL > io_grid.c:#ifdef BUILD_FOR_RDSOL > io_grid.c:#ifdef BUILD_FOR_RDSOL > io_grid.c:#ifdef BUILD_FOR_RDSOL > io_grid.c:#ifdef BUILD_FOR_RDSOL > io_gridf.F:#ifdef BUILD_FOR_RDSOL > io_gridf.F:#ifdef BUILD_FOR_RDSOL > io_gridf.F:#ifdef BUILD_FOR_RDSOL > score.h:#ifdef BUILD_FOR_RDSOL From teck.m.lim at wmich.edu Tue Jul 8 10:40:24 2008 From: teck.m.lim at wmich.edu (Teck Maan) Date: Tue, 08 Jul 2008 13:40:24 -0400 Subject: [Dock-fans] premature termination Amberscore Message-ID: <1215538824.3437.5.camel@localhost.localdomain> Hi, I was running amber for the protein 2HTY on a molecule that i created. However, it stopped prematurely at "Initializing Library File Routines..." Is there a size limitation for the protein molecules? Thanks in advance. Teck Maan -------------------------------------- DOCK v6.2 Released March 2008 Copyright UCSF -------------------------------------- Molecule Library Input Parameters ------------------------------------------------------------------------------------------ ligand_atom_file lig.amber_score.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no Orient Ligand Parameters ------------------------------------------------------------------------------------------ orient_ligand no Flexible Ligand Parameters ------------------------------------------------------------------------------------------ flexible_ligand no Bump Filter Parameters ------------------------------------------------------------------------------------------ bump_filter no Master Score Parameters ------------------------------------------------------------------------------------------ score_molecules yes Contact Score Parameters ------------------------------------------------------------------------------------------ contact_score_primary no contact_score_secondary no Grid Score Parameters ------------------------------------------------------------------------------------------ grid_score_primary no grid_score_secondary no Dock3.5 Score Parameters ------------------------------------------------------------------------------------------ dock3.5_score_primary no dock3.5_score_secondary no Continuous Energy Score Parameters ------------------------------------------------------------------------------------------ continuous_score_primary no continuous_score_secondary no Zou GB/SA Score Parameters ------------------------------------------------------------------------------------------ gbsa_zou_score_primary no gbsa_zou_score_secondary no Hawkins GB/SA Score Parameters ------------------------------------------------------------------------------------------ gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_primary yes amber_score_secondary no amber_score_receptor_file_prefix 2hty amber_score_movable_region ligand amber_score_minimization_rmsgrad 0.01 amber_score_before_md_minimization_cycles 100 amber_score_md_steps 3000 amber_score_after_md_minimization_cycles 100 amber_score_gb_model 5 amber_score_nonbonded_cutoff 18.0 amber_score_temperature 300.0 amber_score_abort_on_unprepped_ligand yes Warning: No secondary scoring function selected. Molecule Library Output Parameters ------------------------------------------------------------------------------------------ ligand_outfile_prefix output write_orientations no num_scored_conformers 1 rank_ligands no ------------------------------------------------------------------------------------------ Initializing Library File Routines... From sbrozell at scripps.edu Tue Jul 8 12:38:20 2008 From: sbrozell at scripps.edu (Scott Brozell) Date: Tue, 8 Jul 2008 12:38:20 -0700 (PDT) Subject: [Dock-fans] premature termination Amberscore In-Reply-To: <1215538824.3437.5.camel@localhost.localdomain> Message-ID: Hi, Rerun it with the the verbose output flag: -v Scott On Tue, 8 Jul 2008, Teck Maan wrote: > I was running amber for the protein 2HTY on a molecule that i created. > However, it stopped prematurely at "Initializing Library File > Routines..." Is there a size limitation for the protein molecules? > Thanks in advance. > > Teck Maan > > > > -------------------------------------- > DOCK v6.2 > > Released March 2008 > Copyright UCSF > -------------------------------------- > > > Molecule Library Input Parameters > ------------------------------------------------------------------------------------------ > ligand_atom_file > lig.amber_score.mol2 > limit_max_ligands no > skip_molecule no > read_mol_solvation no > calculate_rmsd no > > Orient Ligand Parameters > ------------------------------------------------------------------------------------------ > orient_ligand no > > Flexible Ligand Parameters > ------------------------------------------------------------------------------------------ > flexible_ligand no > > Bump Filter Parameters > ------------------------------------------------------------------------------------------ > bump_filter no > > Master Score Parameters > ------------------------------------------------------------------------------------------ > score_molecules yes > > Contact Score Parameters > ------------------------------------------------------------------------------------------ > contact_score_primary no > contact_score_secondary no > > Grid Score Parameters > ------------------------------------------------------------------------------------------ > grid_score_primary no > grid_score_secondary no > > Dock3.5 Score Parameters > ------------------------------------------------------------------------------------------ > dock3.5_score_primary no > dock3.5_score_secondary no > > Continuous Energy Score Parameters > ------------------------------------------------------------------------------------------ > continuous_score_primary no > continuous_score_secondary no > > Zou GB/SA Score Parameters > ------------------------------------------------------------------------------------------ > gbsa_zou_score_primary no > gbsa_zou_score_secondary no > > Hawkins GB/SA Score Parameters > ------------------------------------------------------------------------------------------ > gbsa_hawkins_score_primary no > gbsa_hawkins_score_secondary no > > Amber Score Parameters > ------------------------------------------------------------------------------------------ > amber_score_primary yes > amber_score_secondary no > amber_score_receptor_file_prefix 2hty > amber_score_movable_region ligand > amber_score_minimization_rmsgrad 0.01 > amber_score_before_md_minimization_cycles 100 > amber_score_md_steps 3000 > amber_score_after_md_minimization_cycles 100 > amber_score_gb_model 5 > amber_score_nonbonded_cutoff 18.0 > amber_score_temperature 300.0 > amber_score_abort_on_unprepped_ligand yes > > Warning: No secondary scoring function selected. > > > Molecule Library Output Parameters > ------------------------------------------------------------------------------------------ > ligand_outfile_prefix output > write_orientations no > num_scored_conformers 1 > rank_ligands no > ------------------------------------------------------------------------------------------ > > Initializing Library File Routines... > From teck.m.lim at wmich.edu Tue Jul 8 11:32:35 2008 From: teck.m.lim at wmich.edu (Teck Maan) Date: Tue, 08 Jul 2008 14:32:35 -0400 Subject: [Dock-fans] premature termination Amberscore In-Reply-To: References: Message-ID: <1215541955.3681.4.camel@localhost.localdomain> Hi, I did with a -v flag. and the result is " Initializing Library File Routines... Initializing Amber_Score... Reading the receptor input files. Reading parm file (2hty.prmtop) Error: unexpected EOF in 2hty.prmtop Error: unexpected EOF in 2hty.prmtop" Any idea where i have done wrong? I remove all the ions, ligands and water. Thanks. On Tue, 2008-07-08 at 12:38 -0700, Scott Brozell wrote: > Hi, > > Rerun it with the the verbose output flag: -v > > Scott > > On Tue, 8 Jul 2008, Teck Maan wrote: > > > I was running amber for the protein 2HTY on a molecule that i created. > > However, it stopped prematurely at "Initializing Library File > > Routines..." Is there a size limitation for the protein molecules? > > Thanks in advance. > > > > Teck Maan > > > > > > > > -------------------------------------- > > DOCK v6.2 > > > > Released March 2008 > > Copyright UCSF > > -------------------------------------- > > > > > > Molecule Library Input Parameters > > ------------------------------------------------------------------------------------------ > > ligand_atom_file > > lig.amber_score.mol2 > > limit_max_ligands no > > skip_molecule no > > read_mol_solvation no > > calculate_rmsd no > > > > Orient Ligand Parameters > > ------------------------------------------------------------------------------------------ > > orient_ligand no > > > > Flexible Ligand Parameters > > ------------------------------------------------------------------------------------------ > > flexible_ligand no > > > > Bump Filter Parameters > > ------------------------------------------------------------------------------------------ > > bump_filter no > > > > Master Score Parameters > > ------------------------------------------------------------------------------------------ > > score_molecules yes > > > > Contact Score Parameters > > ------------------------------------------------------------------------------------------ > > contact_score_primary no > > contact_score_secondary no > > > > Grid Score Parameters > > ------------------------------------------------------------------------------------------ > > grid_score_primary no > > grid_score_secondary no > > > > Dock3.5 Score Parameters > > ------------------------------------------------------------------------------------------ > > dock3.5_score_primary no > > dock3.5_score_secondary no > > > > Continuous Energy Score Parameters > > ------------------------------------------------------------------------------------------ > > continuous_score_primary no > > continuous_score_secondary no > > > > Zou GB/SA Score Parameters > > ------------------------------------------------------------------------------------------ > > gbsa_zou_score_primary no > > gbsa_zou_score_secondary no > > > > Hawkins GB/SA Score Parameters > > ------------------------------------------------------------------------------------------ > > gbsa_hawkins_score_primary no > > gbsa_hawkins_score_secondary no > > > > Amber Score Parameters > > ------------------------------------------------------------------------------------------ > > amber_score_primary yes > > amber_score_secondary no > > amber_score_receptor_file_prefix 2hty > > amber_score_movable_region ligand > > amber_score_minimization_rmsgrad 0.01 > > amber_score_before_md_minimization_cycles 100 > > amber_score_md_steps 3000 > > amber_score_after_md_minimization_cycles 100 > > amber_score_gb_model 5 > > amber_score_nonbonded_cutoff 18.0 > > amber_score_temperature 300.0 > > amber_score_abort_on_unprepped_ligand yes > > > > Warning: No secondary scoring function selected. > > > > > > Molecule Library Output Parameters > > ------------------------------------------------------------------------------------------ > > ligand_outfile_prefix output > > write_orientations no > > num_scored_conformers 1 > > rank_ligands no > > ------------------------------------------------------------------------------------------ > > > > Initializing Library File Routines... > > > From sbrozell at scripps.edu Tue Jul 8 12:57:40 2008 From: sbrozell at scripps.edu (Scott Brozell) Date: Tue, 8 Jul 2008 12:57:40 -0700 (PDT) Subject: [Dock-fans] premature termination Amberscore In-Reply-To: <1215541955.3681.4.camel@localhost.localdomain> Message-ID: Hi, On Tue, 8 Jul 2008, Teck Maan wrote: > I did with a -v flag. and the result is > " > Initializing Library File Routines... > Initializing Amber_Score... > > Reading the receptor input files. > Reading parm file (2hty.prmtop) > Error: unexpected EOF in 2hty.prmtop > Error: unexpected EOF in 2hty.prmtop" > > Any idea where i have done wrong? I remove all the ions, ligands and > water. No, except a general failure in preparation. http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore Did you: In particular, examine the amberize*.out and *.log files for warnings and errors. Experience using AMBER will help in understanding and judging the impact of the messages in these files. Correcting problems may involve substantial effort. See the DOCK Fans mailing list for specific examples. Did you view your receptor in a graphics program: 2hty.prmtop Scott > On Tue, 2008-07-08 at 12:38 -0700, Scott Brozell wrote: > > Hi, > > > > Rerun it with the the verbose output flag: -v > > > > Scott > > > > On Tue, 8 Jul 2008, Teck Maan wrote: > > > > > I was running amber for the protein 2HTY on a molecule that i created. > > > However, it stopped prematurely at "Initializing Library File > > > Routines..." Is there a size limitation for the protein molecules? > > > Thanks in advance. > > > > > > Teck Maan > > > > > > > > > > > > -------------------------------------- > > > DOCK v6.2 > > > > > > Released March 2008 > > > Copyright UCSF > > > -------------------------------------- > > > > > > > > > Molecule Library Input Parameters > > > ------------------------------------------------------------------------------------------ > > > ligand_atom_file > > > lig.amber_score.mol2 > > > limit_max_ligands no > > > skip_molecule no > > > read_mol_solvation no > > > calculate_rmsd no > > > > > > Orient Ligand Parameters > > > ------------------------------------------------------------------------------------------ > > > orient_ligand no > > > > > > Flexible Ligand Parameters > > > ------------------------------------------------------------------------------------------ > > > flexible_ligand no > > > > > > Bump Filter Parameters > > > ------------------------------------------------------------------------------------------ > > > bump_filter no > > > > > > Master Score Parameters > > > ------------------------------------------------------------------------------------------ > > > score_molecules yes > > > > > > Contact Score Parameters > > > ------------------------------------------------------------------------------------------ > > > contact_score_primary no > > > contact_score_secondary no > > > > > > Grid Score Parameters > > > ------------------------------------------------------------------------------------------ > > > grid_score_primary no > > > grid_score_secondary no > > > > > > Dock3.5 Score Parameters > > > ------------------------------------------------------------------------------------------ > > > dock3.5_score_primary no > > > dock3.5_score_secondary no > > > > > > Continuous Energy Score Parameters > > > ------------------------------------------------------------------------------------------ > > > continuous_score_primary no > > > continuous_score_secondary no > > > > > > Zou GB/SA Score Parameters > > > ------------------------------------------------------------------------------------------ > > > gbsa_zou_score_primary no > > > gbsa_zou_score_secondary no > > > > > > Hawkins GB/SA Score Parameters > > > ------------------------------------------------------------------------------------------ > > > gbsa_hawkins_score_primary no > > > gbsa_hawkins_score_secondary no > > > > > > Amber Score Parameters > > > ------------------------------------------------------------------------------------------ > > > amber_score_primary yes > > > amber_score_secondary no > > > amber_score_receptor_file_prefix 2hty > > > amber_score_movable_region ligand > > > amber_score_minimization_rmsgrad 0.01 > > > amber_score_before_md_minimization_cycles 100 > > > amber_score_md_steps 3000 > > > amber_score_after_md_minimization_cycles 100 > > > amber_score_gb_model 5 > > > amber_score_nonbonded_cutoff 18.0 > > > amber_score_temperature 300.0 > > > amber_score_abort_on_unprepped_ligand yes > > > From yolanda.only at yahoo.com.cn Tue Jul 8 19:35:40 2008 From: yolanda.only at yahoo.com.cn (Äî Áõ) Date: Tue, 8 Jul 2008 19:35:40 -0700 (PDT) Subject: [Dock-fans] how to convert mol2 format to sdf format? Message-ID: <632658.94924.qm@web15601.mail.cnb.yahoo.com> Dear dock-fans, I wonder that can DOCK convert mol2 format to sdf format? I have gotten some informations that the accessories of the older versions maybe do it. Does the DOCK6 have this function? Thanks in advance for any help! Best regards, Yolanda Guo Northeast Normal University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20080708/73c58d2a/attachment.html From jji at cgl.ucsf.edu Wed Jul 9 21:53:40 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Wed, 09 Jul 2008 21:53:40 -0700 Subject: [Dock-fans] how to convert mol2 format to sdf format? Message-ID: <487595D4.9050509@cgl.ucsf.edu> Hi Yolanda You wrote: I wonder that can DOCK convert mol2 format to sdf format? I have gotten some informations that the accessories of the older versions maybe do it. Does the DOCK6 have this function? I don't think DOCK can do it, but many other programs can. If you do not want to get OEChem, OpenBabel, CDK, Marvin, or any of the many other programs that can do this, you can use the website http://cdb.ics.uci.edu/CHEM/Web/cgibin/BabelWeb.py which is a free OpenBabel file format converter. Cool, eh? John UCSF DOCK Team From yolanda.only at yahoo.com.cn Thu Jul 10 23:58:03 2008 From: yolanda.only at yahoo.com.cn (Äî Áõ) Date: Thu, 10 Jul 2008 23:58:03 -0700 (PDT) Subject: [Dock-fans] something about clustering Message-ID: <742421.13728.qm@web15608.mail.cnb.yahoo.com> Dear dock-fans, Thanks very much for John's advice and I have tried SUBSET 1.0 to do clustering. But I don't know how to prepare the input files for SUBSET. Though the SUBSET introduction suggested that the CACTVS subdirectory contains a TCL script useful to generate SUBSET input files, I still can't understand it very well. I have been puzzled for several days. I know maybe this question is not pertaining to DOCK, but I really need some help from dock-fans. Thanks for your patience and any answer would be appreciate! Best regards, Yolanda Guo Northeast Normal University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20080710/bb63a0ec/attachment.html From d1xu at ucsd.edu Fri Jul 11 01:37:22 2008 From: d1xu at ucsd.edu (Dong Xu) Date: Fri, 11 Jul 2008 01:37:22 -0700 Subject: [Dock-fans] de novo drug design Message-ID: <14da35910807110137g6fdd2cfegf11ff2395eefae0f@mail.gmail.com> Hi Dock fans, Are there are freely available de novo drug design tools that can be used along with Dock? I'm interested in tools that do core/scaffold hopping and pharmacophore. Thanks! -DX -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20080711/ecb92796/attachment.html From awiser at ucsc.edu Fri Jul 11 12:34:24 2008 From: awiser at ucsc.edu (Andrew Harris Wiser) Date: Fri, 11 Jul 2008 12:34:24 -0700 Subject: [Dock-fans] how to convert mol2 format to sdf format? Message-ID: Hi Yolanda, One of the issues I ran into when converting Dock results from mol2 to sdf was extracting the scores from the comment fields for each compound. I tried performing conversions in both openbabel and Pipeline Pilot, but in both cases the comment fields were lost making analysis of the results outside of ViewDock tedious. I ended up writing a short perl script to extract the comment fields into a tab delimited file that can be easily merged in Pipeline Pilot. While this is an extra step in converting formats, the end result, an sdf file where each compound has properties reflecting the results from Dock, is very useful. This is something I thought you might want to consider in addition to the actual conversion process since some of the data gets lost in translation. I tested the website provided and it too seemed to have this problem. As a side note is there a way to output the scores from Dock into fields that do not require this extra step? I'm still learning Dock, but I didn't see an option to change this. Based on the mol2 format specifications it seemed like mol2 files do not have the freedom of sdf/sd/mol files with property fields. -Andrew Wiser From sbrozell at scripps.edu Fri Jul 11 15:34:38 2008 From: sbrozell at scripps.edu (Scott Brozell) Date: Fri, 11 Jul 2008 15:34:38 -0700 (PDT) Subject: [Dock-fans] how to convert mol2 format to sdf format? In-Reply-To: Message-ID: Hi, On Fri, 11 Jul 2008, Andrew Harris Wiser wrote: > One of the issues I ran into when converting Dock results > from mol2 to sdf was extracting the scores from the > comment fields for each compound. I tried performing > conversions in both openbabel and Pipeline Pilot, but in > both cases the comment fields were lost making analysis of > the results outside of ViewDock tedious. I ended up > writing a short perl script to extract the comment fields > into a tab delimited file that can be easily merged in > Pipeline Pilot. While this is an extra step in converting > formats, the end result, an sdf file where each compound > has properties reflecting the results from Dock, is very > useful. > > This is something I thought you might want to consider in > addition to the actual conversion process since some of > the data gets lost in translation. I tested the website > provided and it too seemed to have this problem. > > As a side note is there a way to output the scores from > Dock into fields that do not require this extra step? I'm > still learning Dock, but I didn't see an option to change > this. Based on the mol2 format specifications it seemed > like mol2 files do not have the freedom of sdf/sd/mol > files with property fields. No way, except via source code modifications. If you have a specific proposal with an example then we shall consider it. Scott From sbrozell at scripps.edu Tue Jul 15 10:37:44 2008 From: sbrozell at scripps.edu (Scott Brozell) Date: Tue, 15 Jul 2008 10:37:44 -0700 (PDT) Subject: [Dock-fans] amber score citations Message-ID: Hi, Please send me citations to any publication that used Amber Score. I'll summarize. thanks, Scott From mabdu3 at email.uky.edu Tue Jul 15 13:45:02 2008 From: mabdu3 at email.uky.edu (Abdul Hameed, MohamedDiwanMo) Date: Tue, 15 Jul 2008 16:45:02 -0400 Subject: [Dock-fans] Refining Dock output Message-ID: <62D3F106CB16C34D825A1B75EFBA68390167884901@EX7FM04.ad.uky.edu> Hello everyone, I did a docking study and have some 8000 docked/ranked molecules as output. I would like to retain only the first 3000 molecules from these ranked ligands. Can anyone tell me how I can do it? Is it possible to take only the top 3000 molecules from this output set? Any suggestions will be helpful. Thank you, Diwan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20080715/709147ff/attachment.html From wipke at chemistry.ucsc.edu Tue Jul 15 14:00:12 2008 From: wipke at chemistry.ucsc.edu (Todd Wipke) Date: Tue, 15 Jul 2008 14:00:12 -0700 (PDT) Subject: [Dock-fans] Refining Dock output In-Reply-To: <62D3F106CB16C34D825A1B75EFBA68390167884901@EX7FM04.ad.uky.edu> Message-ID: Sure, convert to SDF file, use Pipeline Pilot and put 3000 in the "Maximum" parameter, then do whatever you want with them, e.g., write to an SDF file. You can also use the Student Edition of Pipeline Pilot which is free to academics. -Todd On Tue, 15 Jul 2008, Abdul Hameed, MohamedDiwanMo wrote: > Hello everyone, > > I did a docking study and have some 8000 docked/ranked molecules as output. > I would like to retain only the first 3000 molecules from these ranked ligands. Can anyone tell me how I can do it? > Is it possible to take only the top 3000 molecules from this output set? > Any suggestions will be helpful. > > Thank you, > Diwan > W. Todd Wipke, Ph.D. Professor of Chemistry and Biochemistry Molecular Engineering Laboratory University of California voice 831-459-2397 Santa Cruz, CA 95064 fax 831-459-2395 http://chemistry.ucsc.edu/wipke_w.html From jji at cgl.ucsf.edu Tue Jul 15 15:28:37 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Tue, 15 Jul 2008 15:28:37 -0700 Subject: [Dock-fans] Refining Dock output In-Reply-To: References: Message-ID: <487D2495.7010504@cgl.ucsf.edu> Hi Diwan You can also do it without Pipeline Pilot in plain old linux: grep -n '@MOL' output.mol2|tail -n +3001|head -1| sed 's/:.*$//' >! cut @ CUT = `cat cut` - 1 head -$CUT output.mol2 >! new.mol2 Happy docking. John UCSF DOCK Team Todd Wipke wrote: > Sure, convert to SDF file, use Pipeline Pilot and put 3000 > in the "Maximum" parameter, then do whatever you want with > them, e.g., write to an SDF file. You can also use the > Student Edition of Pipeline Pilot which is free to > academics. > -Todd > > On Tue, 15 Jul 2008, Abdul Hameed, MohamedDiwanMo wrote: > > >> Hello everyone, >> >> I did a docking study and have some 8000 docked/ranked molecules as output. >> I would like to retain only the first 3000 molecules from these ranked ligands. Can anyone tell me how I can do it? >> Is it possible to take only the top 3000 molecules from this output set? >> Any suggestions will be helpful. >> >> Thank you, >> Diwan >> >> > > W. Todd Wipke, Ph.D. > Professor of Chemistry and Biochemistry > Molecular Engineering Laboratory > University of California voice 831-459-2397 > Santa Cruz, CA 95064 fax 831-459-2395 > http://chemistry.ucsc.edu/wipke_w.html > > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > From mlevesqu at ucsd.edu Tue Jul 15 20:28:47 2008 From: mlevesqu at ucsd.edu (Marshall Levesque) Date: Tue, 15 Jul 2008 20:28:47 -0700 Subject: [Dock-fans] DOCKing with different architectures? Message-ID: <187b4a6e0807152028m9c25b4dv4ea3f17ed108a511@mail.gmail.com> This may be a general question that applies to all of the DOCK software suite, or only certain parts: If one were to perform a screening of 100 small compounds (eg from ZINC) using DOCK6 (grid energy and/or AMBER score) and the workload was split between two different architectures (32-bit/64-bit, different compiler versions), are there any issues with using the results ranked by energy score? For this described situation, 50 compounds screened on each machine, same target, same input files/parameters. I'm asking this because if I run the same set of compounds on two different architectures, I get similar results with similar rankings and scores, but sometimes there is the occasional swing in score for some of the compounds (eg -20 --> -8 for grid energy score). These large changes in score are obviously discomforting, but even the small changes (-20 --> -19) could cause a significant shift in rankings when screen large datasets on the order of 10^5 or 10^6. Those most familiar with the DOCK algorithms might know best. Is the difference in score coming from different architectures something to do with the calculation of the score? or the orientation/confirmation of the compounds by anchor-and-grow? I felt that the limited sampling of the search space results in the fact that one can never produce a TRUE score, but more sampling does narrow the window of discrepancy in energy score for the same compound DOCKed on two different architectures, leading me to believe the conformation search is at fault. Any insight into this would be greatly appreciated, thanks! -Marshall UC San Diego Bioengineering -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20080715/c954439c/attachment.html From jji at cgl.ucsf.edu Wed Jul 16 11:05:09 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Wed, 16 Jul 2008 11:05:09 -0700 Subject: [Dock-fans] DOCKing with different architectures? In-Reply-To: <187b4a6e0807152028m9c25b4dv4ea3f17ed108a511@mail.gmail.com> References: <187b4a6e0807152028m9c25b4dv4ea3f17ed108a511@mail.gmail.com> Message-ID: <487E3855.9030808@cgl.ucsf.edu> Hi Marshall Marshall Levesque wrote: > This may be a general question that applies to all of the DOCK > software suite, or only certain parts: > > If one were to perform a screening of 100 small compounds (eg from > ZINC) using DOCK6 (grid energy and/or AMBER score) and the workload > was split between two different architectures (32-bit/64-bit, > different compiler versions), are there any issues with using the > results ranked by energy score? For this described situation, 50 > compounds screened on each machine, same target, same input > files/parameters. > I'm asking this because if I run the same set of compounds on two > different architectures, I get similar results with similar rankings > and scores, but sometimes there is the occasional swing in score for > some of the compounds (eg -20 --> -8 for grid energy score). These > large changes in score are obviously discomforting, but even the small > changes (-20 --> -19) could cause a significant shift in rankings when > screen large datasets on the order of 10^5 or 10^6. > > Those most familiar with the DOCK algorithms might know best. Is the > difference in score coming from different architectures something to > do with the calculation of the score? or the orientation/confirmation > of the compounds by anchor-and-grow? > > I felt that the limited sampling of the search space results in the > fact that one can never produce a TRUE score, but more sampling does > narrow the window of discrepancy in energy score for the same compound > DOCKed on two different architectures, leading me to believe the > conformation search is at fault. > > Any insight into this would be greatly appreciated, thanks! We use a different version of DOCK, but I think the conclusions are general for the method. It is normal for DOCK to produce very slightly different results for identical input on different hardware due to accumulation of small rounding errors on floating point numbers. Occasionally, the "slight difference" will be at a saddle point during a step of minimization, resulting in a different local minimum being found, and thus, potentially dramatically different results. But you don't have to go to new hardware to see this phenomenon. Just reverse the order of molecules in the database, so that minimization of a compound starts with a different random seed. The bottom line? Docking can be useful, but has important weaknesses. Make predictions, test them, and go back afterwards and check the calculation against the experimental results. I hope this helps. John UCSF DOCK Team From mlevesqu at ucsd.edu Wed Jul 16 11:28:40 2008 From: mlevesqu at ucsd.edu (Marshall Levesque) Date: Wed, 16 Jul 2008 11:28:40 -0700 Subject: [Dock-fans] DOCKing with different architectures? In-Reply-To: <487E3855.9030808@cgl.ucsf.edu> References: <187b4a6e0807152028m9c25b4dv4ea3f17ed108a511@mail.gmail.com> <487E3855.9030808@cgl.ucsf.edu> Message-ID: <187b4a6e0807161128t69825e4bp6f8930c82ec22b99@mail.gmail.com> John- Thank you for the quick and helpful reply. I had assumed this was the cause of discrepancies. So in your opinion, results from a screening experiment that was run on a single machine have equal "validity" when compared to the same screening results obtained using two different architectures? -Marshall On Wed, Jul 16, 2008 at 11:05 AM, John J. Irwin wrote: > Hi Marshall > > Marshall Levesque wrote: > > This may be a general question that applies to all of the DOCK > > software suite, or only certain parts: > > > > If one were to perform a screening of 100 small compounds (eg from > > ZINC) using DOCK6 (grid energy and/or AMBER score) and the workload > > was split between two different architectures (32-bit/64-bit, > > different compiler versions), are there any issues with using the > > results ranked by energy score? For this described situation, 50 > > compounds screened on each machine, same target, same input > > files/parameters. > > I'm asking this because if I run the same set of compounds on two > > different architectures, I get similar results with similar rankings > > and scores, but sometimes there is the occasional swing in score for > > some of the compounds (eg -20 --> -8 for grid energy score). These > > large changes in score are obviously discomforting, but even the small > > changes (-20 --> -19) could cause a significant shift in rankings when > > screen large datasets on the order of 10^5 or 10^6. > > > > Those most familiar with the DOCK algorithms might know best. Is the > > difference in score coming from different architectures something to > > do with the calculation of the score? or the orientation/confirmation > > of the compounds by anchor-and-grow? > > > > I felt that the limited sampling of the search space results in the > > fact that one can never produce a TRUE score, but more sampling does > > narrow the window of discrepancy in energy score for the same compound > > DOCKed on two different architectures, leading me to believe the > > conformation search is at fault. > > > > Any insight into this would be greatly appreciated, thanks! > We use a different version of DOCK, but I think the conclusions are > general for the method. It is normal for DOCK to produce very slightly > different results for identical input on different hardware due to > accumulation of small rounding errors on floating point numbers. > Occasionally, the "slight difference" will be at a saddle point during a > step of minimization, resulting in a different local minimum being > found, and thus, potentially dramatically different results. But you > don't have to go to new hardware to see this phenomenon. Just reverse > the order of molecules in the database, so that minimization of a > compound starts with a different random seed. > > The bottom line? Docking can be useful, but has important weaknesses. > Make predictions, test them, and go back afterwards and check the > calculation against the experimental results. > > I hope this helps. > > John > UCSF DOCK Team > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20080716/d31242b2/attachment.html From snoze.pa at gmail.com Wed Jul 16 11:51:32 2008 From: snoze.pa at gmail.com (snoze pa) Date: Wed, 16 Jul 2008 13:51:32 -0500 Subject: [Dock-fans] dock 6.2 error message Message-ID: <10f848910807161151x5d7228f4tc5b30525fcd2131f@mail.gmail.com> Dear Dockers, I am trying to compile the dock6.2 but getting following error messages in fedora 9. Both stand alone and parallel version are showing following error messages. Any Idea or help? Thanks for your help. s Starting installation of DOCK v6.2 at Wed Jul 16 13:49:10 CDT 2008. cd ../src && make install make[1]: Entering directory `/home/guest/PROG/dock6/src' cd dock && make install make[2]: Entering directory `/home/guest/PROG/dock6/src/dock' g++ -c -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/usr/local/mpich2//include -O2 -o amber_typer.o amber_typer.cpp amber_typer.cpp: In function 'char* white_line(char*)': amber_typer.cpp:16: error: 'strlen' was not declared in this scope amber_typer.cpp: In function 'int assign_node(ATOM_TYPE_NODE&, int)': amber_typer.cpp:67: error: 'strtok' was not declared in this scope amber_typer.cpp:67: error: 'strcpy' was not declared in this scope amber_typer.cpp:88: error: 'strncmp' was not declared in this scope amber_typer.cpp: In function 'int check_type(const char*, const char*)': amber_typer.cpp:126: error: 'strstr' was not declared in this scope amber_typer.cpp: In constructor 'ATOM_TYPE::ATOM_TYPE()': amber_typer.cpp:252: error: 'INT_MIN' was not declared in this scope amber_typer.cpp: In member function 'void ATOM_TYPER::get_vdw_labels(std::string, bool)': amber_typer.cpp:286: error: 'strncmp' was not declared in this scope amber_typer.cpp:347: error: 'strtok' was not declared in this scope amber_typer.cpp:383: error: 'INT_MIN' was not declared in this scope amber_typer.cpp:388: error: 'INT_MIN' was not declared in this scope amber_typer.cpp: In member function 'int ATOM_TYPER::assign_vdw_labels(DOCKMol&, int)': amber_typer.cpp:476: error: 'strcmp' was not declared in this scope amber_typer.cpp: In member function 'void BOND_TYPER::get_flex_labels(std::string)': amber_typer.cpp:532: error: 'strncmp' was not declared in this scope amber_typer.cpp:545: error: 'strlen' was not declared in this scope amber_typer.cpp:562: error: 'strtok' was not declared in this scope amber_typer.cpp: In member function 'void BOND_TYPER::get_flex_search(std::string)': amber_typer.cpp:599: error: 'strtok' was not declared in this scope amber_typer.cpp:601: error: 'strcmp' was not declared in this scope amber_typer.cpp: In member function 'void CHEM_TYPER::get_chem_labels(std::string)': amber_typer.cpp:754: error: 'strncmp' was not declared in this scope amber_typer.cpp:763: error: 'strtok' was not declared in this scope make[2]: *** [amber_typer.o] Error 1 From jji at cgl.ucsf.edu Wed Jul 16 12:10:33 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Wed, 16 Jul 2008 12:10:33 -0700 Subject: [Dock-fans] de novo drug design In-Reply-To: <14da35910807110137g6fdd2cfegf11ff2395eefae0f@mail.gmail.com> References: <14da35910807110137g6fdd2cfegf11ff2395eefae0f@mail.gmail.com> Message-ID: <487E47A9.3060800@cgl.ucsf.edu> Hi DX I don't know of any free de novo design tools. I do know about Allegrow http://bostondenovo.com/ and Sprout http://www.simbiosys.ca/, but have no idea about price. For scaffold hopping, try ROCS/EON from OpenEye (http://eyesopen.com/) which is a shape approach, and is free to accredited academics. OE also have a tool for directly mutating one atom at a time, BROOD, but it may be a challenge to test some of those suggestions experimentally. Cactvs is free to academics and incorporates fingerprint methods that can be use to essentially scaffold hop (find similar molecules). molinspiration.com is free to academics and has a tool to break up molecules into fragments, which is a useful underlying technology for scaffold hopping. Of course, none of these programs works directly with DOCK - I interpreted your "can be used along with" liberally. John UCSF DOCK Team Dong Xu wrote: > Hi Dock fans, > > Are there are freely available de novo drug design tools that can be > used along with Dock? I'm interested in tools that do core/scaffold > hopping and pharmacophore. > > Thanks! > > -DX > ------------------------------------------------------------------------ > > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > From jji at cgl.ucsf.edu Wed Jul 16 12:18:27 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Wed, 16 Jul 2008 12:18:27 -0700 Subject: [Dock-fans] DOCKing with different architectures? In-Reply-To: <187b4a6e0807161128t69825e4bp6f8930c82ec22b99@mail.gmail.com> References: <187b4a6e0807152028m9c25b4dv4ea3f17ed108a511@mail.gmail.com> <487E3855.9030808@cgl.ucsf.edu> <187b4a6e0807161128t69825e4bp6f8930c82ec22b99@mail.gmail.com> Message-ID: <487E4983.5060805@cgl.ucsf.edu> Hi Marshall Marshall Levesque wrote: > John- > > Thank you for the quick and helpful reply. > > I had assumed this was the cause of discrepancies. So in your > opinion, results from a screening experiment that was run on a single > machine have equal "validity" when compared to the same screening > results obtained using two different architectures? Yes, equally "valid", by which I mean, they have no "validity" at all. What does it mean to say a docking prediction is valid? It means it actually works against the enzyme. Thus, they are predictions that need to be tested. John UCSF DOCK Team > > -Marshall > > On Wed, Jul 16, 2008 at 11:05 AM, John J. Irwin > wrote: > > Hi Marshall > > Marshall Levesque wrote: > > This may be a general question that applies to all of the DOCK > > software suite, or only certain parts: > > > > If one were to perform a screening of 100 small compounds (eg from > > ZINC) using DOCK6 (grid energy and/or AMBER score) and the workload > > was split between two different architectures (32-bit/64-bit, > > different compiler versions), are there any issues with using the > > results ranked by energy score? For this described situation, 50 > > compounds screened on each machine, same target, same input > > files/parameters. > > I'm asking this because if I run the same set of compounds on two > > different architectures, I get similar results with similar rankings > > and scores, but sometimes there is the occasional swing in score for > > some of the compounds (eg -20 --> -8 for grid energy score). These > > large changes in score are obviously discomforting, but even the > small > > changes (-20 --> -19) could cause a significant shift in > rankings when > > screen large datasets on the order of 10^5 or 10^6. > > > > Those most familiar with the DOCK algorithms might know best. > Is the > > difference in score coming from different architectures something to > > do with the calculation of the score? or the > orientation/confirmation > > of the compounds by anchor-and-grow? > > > > I felt that the limited sampling of the search space results in the > > fact that one can never produce a TRUE score, but more sampling does > > narrow the window of discrepancy in energy score for the same > compound > > DOCKed on two different architectures, leading me to believe the > > conformation search is at fault. > > > > Any insight into this would be greatly appreciated, thanks! > We use a different version of DOCK, but I think the conclusions are > general for the method. It is normal for DOCK to produce very slightly > different results for identical input on different hardware due to > accumulation of small rounding errors on floating point numbers. > Occasionally, the "slight difference" will be at a saddle point > during a > step of minimization, resulting in a different local minimum being > found, and thus, potentially dramatically different results. But you > don't have to go to new hardware to see this phenomenon. Just reverse > the order of molecules in the database, so that minimization of a > compound starts with a different random seed. > > The bottom line? Docking can be useful, but has important weaknesses. > Make predictions, test them, and go back afterwards and check the > calculation against the experimental results. > > I hope this helps. > > John > UCSF DOCK Team > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > > From biopolak at yahoo.co.uk Wed Jul 16 12:26:15 2008 From: biopolak at yahoo.co.uk (Peter Oledzki) Date: Wed, 16 Jul 2008 20:26:15 +0100 (BST) Subject: [Dock-fans] de novo drug design In-Reply-To: <487E47A9.3060800@cgl.ucsf.edu> Message-ID: <112461.63666.qm@web23003.mail.ird.yahoo.com> Hi, BioSolveIT - http://www.biosolveit.de/software/libraries.html do de novo software but this is also not free. Recore provides scaffold replacement with pocket spheres and pharmacophore constraints. Peter --- "John J. Irwin" wrote: > Hi DX > > I don't know of any free de novo design tools. I do > know about Allegrow > http://bostondenovo.com/ and Sprout > http://www.simbiosys.ca/, but have > no idea about price. > > For scaffold hopping, try ROCS/EON from OpenEye > (http://eyesopen.com/) > which is a shape approach, and is free to accredited > academics. OE also > have a tool for directly mutating one atom at a > time, BROOD, but it may > be a challenge to test some of those suggestions > experimentally. Cactvs > is free to academics and incorporates fingerprint > methods that can be > use to essentially scaffold hop (find similar > molecules). > molinspiration.com is free to academics and has a > tool to break up > molecules into fragments, which is a useful > underlying technology for > scaffold hopping. > > Of course, none of these programs works directly > with DOCK - I > interpreted your "can be used along with" liberally. > > John > UCSF DOCK Team > > > Dong Xu wrote: > > Hi Dock fans, > > > > Are there are freely available de novo drug design > tools that can be > > used along with Dock? I'm interested in tools that > do core/scaffold > > hopping and pharmacophore. > > > > Thanks! > > > > -DX > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Dock-fans mailing list > > Dock-fans at docking.org > > > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > > > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > __________________________________________________________ Not happy with your email address?. Get the one you really want - millions of new email addresses available now at Yahoo! http://uk.docs.yahoo.com/ymail/new.html From snoze.pa at gmail.com Wed Jul 16 12:37:20 2008 From: snoze.pa at gmail.com (snoze pa) Date: Wed, 16 Jul 2008 14:37:20 -0500 Subject: [Dock-fans] dock 6.2 error message In-Reply-To: <10f848910807161151x5d7228f4tc5b30525fcd2131f@mail.gmail.com> References: <10f848910807161151x5d7228f4tc5b30525fcd2131f@mail.gmail.com> Message-ID: <10f848910807161237l4c9743fdraaf18259ac15b908@mail.gmail.com> Fixed the problem after adding these headers #include #include in following files. amber_typer.cpp conf_gen.cpp dockmol.cpp library_file.cpp orient.cpp score.cpp simplex.cpp .. .. etc On Wed, Jul 16, 2008 at 1:51 PM, snoze pa wrote: > Dear Dockers, > I am trying to compile the dock6.2 but getting following error > messages in fedora 9. Both stand alone and parallel version are > showing following error messages. > Any Idea or help? Thanks for your help. > s > > > Starting installation of > DOCK v6.2 > at Wed Jul 16 13:49:10 CDT 2008. > > cd ../src && make install > make[1]: Entering directory `/home/guest/PROG/dock6/src' > cd dock && make install > make[2]: Entering directory `/home/guest/PROG/dock6/src/dock' > g++ -c -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK > -DMPICH_SKIP_MPICXX -I/usr/local/mpich2//include -O2 -o amber_typer.o > amber_typer.cpp > amber_typer.cpp: In function 'char* white_line(char*)': > amber_typer.cpp:16: error: 'strlen' was not declared in this scope > amber_typer.cpp: In function 'int assign_node(ATOM_TYPE_NODE&, int)': > amber_typer.cpp:67: error: 'strtok' was not declared in this scope > amber_typer.cpp:67: error: 'strcpy' was not declared in this scope > amber_typer.cpp:88: error: 'strncmp' was not declared in this scope > amber_typer.cpp: In function 'int check_type(const char*, const char*)': > amber_typer.cpp:126: error: 'strstr' was not declared in this scope > amber_typer.cpp: In constructor 'ATOM_TYPE::ATOM_TYPE()': > amber_typer.cpp:252: error: 'INT_MIN' was not declared in this scope > amber_typer.cpp: In member function 'void > ATOM_TYPER::get_vdw_labels(std::string, bool)': > amber_typer.cpp:286: error: 'strncmp' was not declared in this scope > amber_typer.cpp:347: error: 'strtok' was not declared in this scope > amber_typer.cpp:383: error: 'INT_MIN' was not declared in this scope > amber_typer.cpp:388: error: 'INT_MIN' was not declared in this scope > amber_typer.cpp: In member function 'int > ATOM_TYPER::assign_vdw_labels(DOCKMol&, int)': > amber_typer.cpp:476: error: 'strcmp' was not declared in this scope > amber_typer.cpp: In member function 'void > BOND_TYPER::get_flex_labels(std::string)': > amber_typer.cpp:532: error: 'strncmp' was not declared in this scope > amber_typer.cpp:545: error: 'strlen' was not declared in this scope > amber_typer.cpp:562: error: 'strtok' was not declared in this scope > amber_typer.cpp: In member function 'void > BOND_TYPER::get_flex_search(std::string)': > amber_typer.cpp:599: error: 'strtok' was not declared in this scope > amber_typer.cpp:601: error: 'strcmp' was not declared in this scope > amber_typer.cpp: In member function 'void > CHEM_TYPER::get_chem_labels(std::string)': > amber_typer.cpp:754: error: 'strncmp' was not declared in this scope > amber_typer.cpp:763: error: 'strtok' was not declared in this scope > make[2]: *** [amber_typer.o] Error 1 > From d1xu at ucsd.edu Wed Jul 16 18:48:19 2008 From: d1xu at ucsd.edu (Dong Xu) Date: Wed, 16 Jul 2008 18:48:19 -0700 Subject: [Dock-fans] de novo drug design In-Reply-To: <487E47A9.3060800@cgl.ucsf.edu> References: <14da35910807110137g6fdd2cfegf11ff2395eefae0f@mail.gmail.com> <487E47A9.3060800@cgl.ucsf.edu> Message-ID: <14da35910807161848l63821689t77070de2a293a505@mail.gmail.com> Hi John, Thanks for all the info! I will check them out. For Cactvs, is this the right link? http://www2.ccc.uni-erlangen.de/software/cactvs/index.html -DX On Wed, Jul 16, 2008 at 12:10 PM, John J. Irwin wrote: > Hi DX > > I don't know of any free de novo design tools. I do know about Allegrow > http://bostondenovo.com/ and Sprout http://www.simbiosys.ca/, but have no > idea about price. > > For scaffold hopping, try ROCS/EON from OpenEye (http://eyesopen.com/) > which is a shape approach, and is free to accredited academics. OE also have > a tool for directly mutating one atom at a time, BROOD, but it may be a > challenge to test some of those suggestions experimentally. Cactvs is free > to academics and incorporates fingerprint methods that can be use to > essentially scaffold hop (find similar molecules). molinspiration.com is > free to academics and has a tool to break up molecules into fragments, which > is a useful underlying technology for scaffold hopping. > > Of course, none of these programs works directly with DOCK - I interpreted > your "can be used along with" liberally. > > John > UCSF DOCK Team > > > Dong Xu wrote: > >> Hi Dock fans, >> >> Are there are freely available de novo drug design tools that can be used >> along with Dock? I'm interested in tools that do core/scaffold hopping and >> pharmacophore. >> >> Thanks! >> >> -DX >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Dock-fans mailing list >> Dock-fans at docking.org >> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20080716/19a1fbfe/attachment.html From Mark.Agostino at vcp.monash.edu.au Wed Jul 16 19:14:22 2008 From: Mark.Agostino at vcp.monash.edu.au (Mark J. Agostino) Date: Thu, 17 Jul 2008 12:14:22 +1000 Subject: [Dock-fans] Carbohydrate docking in DOCK 6.2 Message-ID: <89907EA1DCFB7548A431C13A270F9DD502DF872F@prk-exch-01.vcp.local> Hello, I have been trying to dock carbohydrates (2 to 4 saccharides in length) using DOCK 6.2 and am getting ridiculous results. I am seeing major steric clash between the saccharide rings. I have tried a multitude of things to fix the problem, including: - Increasing number of minimisation steps (simplex_max_iterations, simplex_final_min_max_iterations and simplex_anchor_max_iterations) - Turning on minimize_flexible_growth - Changing anchor size (used 6 and 40) - Selected more spheres for binding site (slightly expanded from cavity) - Changed repulsive exponent in grid generation and docking run from 12 to 9 (repulsive_exponent in GRID input file and internal_energy_rep_exp in DOCK input file) - Adjusted flex.defn to allow minimisation of some additional torsions (conj-oxygen and sp2-aromatic) - Adjusted flex.defn to explicitly specify minimisation of glycosidic linkages (shown below) name carb1 drive_id 8 minimize 1 definition C.3 ( H ) ( 2 O ) definition O ( C.3 ( H ) ) name carb2 drive_id 8 minimize 1 definition C.3 ( H ) ( 2 C. ) definition O ( C.3 ( H ) ) but none of this seems to generate good structures. The structures at the end look as if they have been crumpled up into a ball and placed in the binding site. I know that DOCK 4.0 used to work fine to dock carbohydrate structures, but now this seems somewhat broken in DOCK 6.2. Is there something I am overlooking here or is the problem something deeper in the program? Thanks in advance, Mark Agostino -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20080717/d3b4adfb/attachment-0001.html From Yunierkis at uclv.edu.cu Thu Jul 17 06:56:17 2008 From: Yunierkis at uclv.edu.cu (Yunierkis Perez Castillo) Date: Thu, 17 Jul 2008 09:56:17 -0400 Subject: [Dock-fans] Carbohydrate docking in DOCK 6.2 In-Reply-To: <89907EA1DCFB7548A431C13A270F9DD502DF872F@prk-exch-01.vcp.local> References: <89907EA1DCFB7548A431C13A270F9DD502DF872F@prk-exch-01.vcp.local> Message-ID: <337193151BB0EF48B8751A82851C804FA567295E@mail-1.uclv.edu.cu> I have found the same "strange" results with DOCK 6.2 when trying to dock small molecules, try 6.1, I get more realistic results with it than with 6.2 Yunierkis ________________________________________ From: dock-fans-bounces at docking.org [dock-fans-bounces at docking.org] On Behalf Of Mark J. Agostino [Mark.Agostino at vcp.monash.edu.au] Sent: Wednesday, July 16, 2008 10:14 PM To: dock-fans at docking.org Subject: [Dock-fans] Carbohydrate docking in DOCK 6.2 Hello, I have been trying to dock carbohydrates (2 to 4 saccharides in length) using DOCK 6.2 and am getting ridiculous results. I am seeing major steric clash between the saccharide rings. I have tried a multitude of things to fix the problem, including: - Increasing number of minimisation steps (simplex_max_iterations, simplex_final_min_max_iterations and simplex_anchor_max_iterations) - Turning on minimize_flexible_growth - Changing anchor size (used 6 and 40) - Selected more spheres for binding site (slightly expanded from cavity) - Changed repulsive exponent in grid generation and docking run from 12 to 9 (repulsive_exponent in GRID input file and internal_energy_rep_exp in DOCK input file) - Adjusted flex.defn to allow minimisation of some additional torsions (conj-oxygen and sp2-aromatic) - Adjusted flex.defn to explicitly specify minimisation of glycosidic linkages (shown below) name carb1 drive_id 8 minimize 1 definition C.3 ( H ) ( 2 O ) definition O ( C.3 ( H ) ) name carb2 drive_id 8 minimize 1 definition C.3 ( H ) ( 2 C. ) definition O ( C.3 ( H ) ) but none of this seems to generate good structures. The structures at the end look as if they have been crumpled up into a ball and placed in the binding site. I know that DOCK 4.0 used to work fine to dock carbohydrate structures, but now this seems somewhat broken in DOCK 6.2. Is there something I am overlooking here or is the problem something deeper in the program? Thanks in advance, Mark Agostino ________________________________ Servicio de Correos de la Universidad Central "Marta Abreu" de Las Villas. http://www.uclv.edu.cu -VI Conferencia Internacional de Ciencias Empresariales, del 16 al 18 de octubre de 2008, Cayo Santa Mar?a, Cuba. http://economia-publica.uab.es/VIcubaCICE.doc -V Conferencia Cient?fica Internacional de Ingenier?a Mec?nica, COMEC 2008, del 4 al 6 de noviembre de 2008, UCLV, Cuba. http://eventos.fim.uclv.edu.cu/comec Servicio de Correos de la Universidad Central "Marta Abreu" de Las Villas. http://www.uclv.edu.cu -VI Conferencia Internacional de Ciencias Empresariales, del 16 al 18 de octubre de 2008, Cayo Santa Mar?a, Cuba. http://economia-publica.uab.es/VIcubaCICE.doc -V Conferencia Cient?fica Internacional de Ingenier?a Mec?nica, COMEC 2008, del 4 al 6 de noviembre de 2008, UCLV, Cuba. http://eventos.fim.uclv.edu.cu/comec From jji at cgl.ucsf.edu Thu Jul 17 10:15:55 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Thu, 17 Jul 2008 10:15:55 -0700 Subject: [Dock-fans] de novo drug design In-Reply-To: <14da35910807161848l63821689t77070de2a293a505@mail.gmail.com> References: <14da35910807110137g6fdd2cfegf11ff2395eefae0f@mail.gmail.com> <487E47A9.3060800@cgl.ucsf.edu> <14da35910807161848l63821689t77070de2a293a505@mail.gmail.com> Message-ID: <487F7E4B.70208@cgl.ucsf.edu> Hi DX Cactvs is at http://xemistry.com/. John Dong Xu wrote: > Hi John, > > Thanks for all the info! I will check them out. For Cactvs, is this > the right link? > > http://www2.ccc.uni-erlangen.de/software/cactvs/index.html > > -DX > > On Wed, Jul 16, 2008 at 12:10 PM, John J. Irwin > wrote: > > Hi DX > > I don't know of any free de novo design tools. I do know about > Allegrow http://bostondenovo.com/ and Sprout > http://www.simbiosys.ca/, but have no idea about price. > > For scaffold hopping, try ROCS/EON from OpenEye > (http://eyesopen.com/) which is a shape approach, and is free to > accredited academics. OE also have a tool for directly mutating > one atom at a time, BROOD, but it may be a challenge to test some > of those suggestions experimentally. Cactvs is free to academics > and incorporates fingerprint methods that can be use to > essentially scaffold hop (find similar molecules). > molinspiration.com is free to > academics and has a tool to break up molecules into fragments, > which is a useful underlying technology for scaffold hopping. > > Of course, none of these programs works directly with DOCK - I > interpreted your "can be used along with" liberally. > > John > UCSF DOCK Team > > > Dong Xu wrote: > > Hi Dock fans, > > Are there are freely available de novo drug design tools that > can be used along with Dock? I'm interested in tools that do > core/scaffold hopping and pharmacophore. > > Thanks! > > -DX > ------------------------------------------------------------------------ > > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > > > From shino6483 at hotmail.com Mon Jul 21 23:29:12 2008 From: shino6483 at hotmail.com (=?ks_c_5601-1987?B?vcW/9cjx?=) Date: Tue, 22 Jul 2008 15:29:12 +0900 Subject: [Dock-fans] metal containing protein Message-ID: Hello everyone. I want to do virtual screening to protein that metal exist at active site. But, I don't have any experience how to treat such a target. I use Dock 4.0 and Dock 5.4. Please help me to know how to treat. _________________________________________________________________ MSN ???? ??? ??, Windows Live Messenger! http://windowslive.msn.co.kr/wlm/messenger/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20080722/0d12db92/attachment.html From jji at cgl.ucsf.edu Tue Jul 22 08:12:10 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Tue, 22 Jul 2008 08:12:10 -0700 Subject: [Dock-fans] metal containing protein In-Reply-To: References: Message-ID: <4885F8CA.9070306@cgl.ucsf.edu> Hi - Metalloenzymes are often more challenging than non-metal-containing enzymes, but with care, they can be made to produce useful results, at least sometimes. For recent papers on docking to metalloenzymes, please see some of the papers from our group (below). There are also of course many other papers - I just know these ones best. Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM. Structure-based activity prediction for an enzyme of unknown function. /Nature/* 448* (7155), 775-9 (2007). Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ, Shoichet BK. Predicting Substrates by Docking High-Energy Intermediates to Enzyme Structures. /J Am Chem Soc/* 128* (49), 15882-891 (2006). Irwin JJ, Raushel FM, Shoichet BK. Virtual screening against metalloenzymes for inhibitors and substrates. /Biochemistry/* 44* (37), 12316-28 (2005). Happy docking John UCSF DOCK Team ??? wrote: > Hello everyone. > > I want to do virtual screening to protein that metal exist at active site. > > But, I don't have any experience how to treat such a target. > > I use Dock 4.0 and Dock 5.4. > > Please help me to know how to treat. > > > > ------------------------------------------------------------------------ > ??? ?? ?? ??? ?? ?? ???, ???? ?? ??? ??? > ?! MSN ???? ??? ??, Windows Live Messenger! > > ------------------------------------------------------------------------ > > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > From ruhul014 at yahoo.com Fri Jul 25 06:43:03 2008 From: ruhul014 at yahoo.com (Ruhul Amin) Date: Fri, 25 Jul 2008 06:43:03 -0700 (PDT) Subject: [Dock-fans] Free docking programs for windows Message-ID: <801991.12815.qm@web51711.mail.re2.yahoo.com> Hi, Can anyone tell me please which docking programs are better that runs on windows xp and free for academic users? Thank you, Ruhul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20080725/05819a6f/attachment.html From jji at cgl.ucsf.edu Fri Jul 25 10:44:57 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Fri, 25 Jul 2008 10:44:57 -0700 Subject: [Dock-fans] Free docking programs for windows In-Reply-To: <801991.12815.qm@web51711.mail.re2.yahoo.com> References: <801991.12815.qm@web51711.mail.re2.yahoo.com> Message-ID: <488A1119.4090605@cgl.ucsf.edu> Hi Ruhul If you can get the source, you should be able to get most docking programs to run on Windows, under cygwin. For instance, to make DOCK on windows, please refer to our wiki. http://wiki.compbio.ucsf.edu/wiki/index.php/DOCK_on_cygwin DOCK is free to academics, and will run happily on Windows, under Cygwin. As you know, there are many docking programs to choose from, and different people have different views. Writing to dock-fans, one should not expect an unbias opinion. One way to get an idea of which docking programs might work best for you is to use the literature. There are many papers that attempt to compare docking programs, but a good place might be Warren (below). Next, look for papers that report the discovery of novel ligands (if that is what you are interested in), paying particular attention to those that report crystal structures. A review that mentions some of these is Shoichet, below. Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS. A critical assessment of docking programs and scoring functions. J Med Chem. 2006 Oct 5;49(20):5912-31. Shoichet BK. Virtual screening of chemical libraries. Nature. 2004 Dec 16;432(7019):862-5. Review. Good docking! John UCSF DOCK Team Ruhul Amin wrote: > Hi, > > Can anyone tell me please which docking programs are better that runs > on windows xp and free for academic users? > > Thank you, > > Ruhul > > From scisoft at rc.usf.edu Mon Jul 28 11:30:50 2008 From: scisoft at rc.usf.edu (Scientific Software Division @ USF-RC) Date: Mon, 28 Jul 2008 14:30:50 -0400 Subject: [Dock-fans] Multiprocessor Test Job Message-ID: <488E105A.4030207@rc.usf.edu> I was wondering if there was anyone out there who would be willing to let me have a sample multiprocessor Dock6 job with expected output. The test suite on the Dock6 website is only for Dock5. Thanks for any help. - Paul Tittle Research Computing @ USF From sudmukh at yahoo.com Mon Jul 28 12:01:12 2008 From: sudmukh at yahoo.com (Sudipto Mukherjee) Date: Mon, 28 Jul 2008 12:01:12 -0700 (PDT) Subject: [Dock-fans] Multiprocessor Test Job Message-ID: <633482.17865.qm@web36705.mail.mud.yahoo.com> Paul, You could use the sample MPI job listed under dock6/tutorials/mpi_demo under your dock6 installation. This tutorial should work out of the box for DOCK6. Regards Sudipto Mukherjee Graduate Student, Robert C. Rizzo Lab Dept. of Applied Math & Statistics, Stony Brook University ----- Original Message ---- From: "Scientific Software Division @ USF-RC" To: dock-fans at docking.org Sent: Monday, July 28, 2008 2:30:50 PM Subject: [Dock-fans] Multiprocessor Test Job I was wondering if there was anyone out there who would be willing to let me have a sample multiprocessor Dock6 job with expected output. The test suite on the Dock6 website is only for Dock5. Thanks for any help. - Paul Tittle Research Computing @ USF _______________________________________________ Dock-fans mailing list Dock-fans at docking.org http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20080728/77d6d6d6/attachment-0001.html From scisoft at rc.usf.edu Mon Jul 28 12:17:12 2008 From: scisoft at rc.usf.edu (Scientific Software Division @ USF-RC) Date: Mon, 28 Jul 2008 15:17:12 -0400 Subject: [Dock-fans] Multiprocessor Test Job In-Reply-To: <633482.17865.qm@web36705.mail.mud.yahoo.com> References: <633482.17865.qm@web36705.mail.mud.yahoo.com> Message-ID: <488E1B38.7000401@rc.usf.edu> Unfortunately, the only problem with that tutorial is that it doesn't come with the expected output. If I had that, then I would be all set. Sudipto Mukherjee wrote: > Paul, > > You could use the sample MPI job listed under dock6/tutorials/mpi_demo > under your dock6 installation. This tutorial should work out of the > box for DOCK6. > > Regards > Sudipto Mukherjee > Graduate Student, Robert C. Rizzo Lab > Dept. of Applied Math & Statistics, Stony Brook University > > ----- Original Message ---- > From: "Scientific Software Division @ USF-RC" > To: dock-fans at docking.org > Sent: Monday, July 28, 2008 2:30:50 PM > Subject: [Dock-fans] Multiprocessor Test Job > > I was wondering if there was anyone out there who would be willing to > let me have a sample multiprocessor Dock6 job with expected output. The > test suite on the Dock6 website is only for Dock5. Thanks for any help. > > - Paul Tittle > Research Computing @ USF > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > From sbrozell at scripps.edu Tue Jul 29 20:15:50 2008 From: sbrozell at scripps.edu (Scott Brozell) Date: Tue, 29 Jul 2008 20:15:50 -0700 (PDT) Subject: [Dock-fans] Multiprocessor Test Job In-Reply-To: <488E1B38.7000401@rc.usf.edu> Message-ID: Hi, [scott]$ ./script_clean [scott]$ ll 4 -rw-r--r-- 1 scott kuntz 734 Mar 27 2006 0README 4 -rw-r--r-- 1 scott kuntz 3955 Mar 2 00:15 mpi.in 4 -rwxr-xr-x 1 scott kuntz 49 Jun 15 2006 script_clean 4 -rwxr-xr-x 1 scott kuntz 982 Jun 15 2006 script_demo [scott]$ ./script_demo Environment variable DOCK_PROCESSES is not defined. Using 4 MPI processes for DOCK. Environment variable MPICH_HOME is defined. Using MPICH mpirun from /home/terry/mpich2-install/bin Starting MPI DOCK. Initializing MPI Routines... Initializing MPI Routines... Initializing MPI Routines... Initializing MPI Routines... [scott]$ ll 4 -rw-r--r-- 1 scott kuntz 734 Mar 27 2006 0README 24 -rw-r--r-- 1 scott kuntz 23819 Jul 29 18:59 1VRT_scored.mol2 4 -rw-r--r-- 1 scott kuntz 3955 Mar 2 00:15 mpi.in 12 -rw-r--r-- 1 scott kuntz 8417 Jul 29 18:59 mpi.out 8 -rw-r--r-- 1 scott kuntz 6539 Jul 29 18:59 mpi.out.1 8 -rw-r--r-- 1 scott kuntz 6540 Jul 29 18:59 mpi.out.2 8 -rw-r--r-- 1 scott kuntz 6637 Jul 29 18:59 mpi.out.3 4 -rwxr-xr-x 1 scott kuntz 49 Jun 15 2006 script_clean 4 -rwxr-xr-x 1 scott kuntz 982 Jun 15 2006 script_demo The run takes 2.5 minutes on a Xeon(TM) CPU 3GHz with TWO processors. I'll email you a tarball. Scott On Mon, 28 Jul 2008, Scientific Software Division @ USF-RC wrote: > Unfortunately, the only problem with that tutorial is that it doesn't > come with the expected output. If I had that, then I would be all set. > > Sudipto Mukherjee wrote: > > Paul, > > > > You could use the sample MPI job listed under dock6/tutorials/mpi_demo > > under your dock6 installation. This tutorial should work out of the > > box for DOCK6. > > > > Regards > > Sudipto Mukherjee > > Graduate Student, Robert C. Rizzo Lab > > Dept. of Applied Math & Statistics, Stony Brook University > > > > ----- Original Message ---- > > From: "Scientific Software Division @ USF-RC" > > To: dock-fans at docking.org > > Sent: Monday, July 28, 2008 2:30:50 PM > > Subject: [Dock-fans] Multiprocessor Test Job > > > > I was wondering if there was anyone out there who would be willing to > > let me have a sample multiprocessor Dock6 job with expected output. The > > test suite on the Dock6 website is only for Dock5. Thanks for any help. > > > > - Paul Tittle > > Research Computing @ USF