From sbrozell at rci.rutgers.edu Tue Nov 3 12:29:39 2009 From: sbrozell at rci.rutgers.edu (Scott Brozell) Date: Tue, 3 Nov 2009 15:29:39 -0500 Subject: [Dock-fans] INSPH part 3 In-Reply-To: References: Message-ID: <20091103202939.GI11475@casegroup.rutgers.edu> Hi, On Mon, Oct 26, 2009 at 03:51:49PM -0400, David Taylor wrote: > Even better. I deleted the other INSPH files and made a new one myself. Then > I did: > > INPUT: /home/molecular/Desktop/dock6/bin/sphgen -i INSPH -o OUTSPH > > OUTPUT: open: No such file or directory > apparent state: unit 4 named 1LAH.ms > lately reading sequential formatted external IO > Aborted > > Not only that, but it created an OUTSPH file with nothing in it! I really > don't know what's going on now! Does the 1LAH.ms file have to be in the same > folder as sphgen or does it need to be in a different one? Right now I have > one in the same folder, but I have no idea where I actually NEED one. You have probably resolved this by now. If not then start with the tutorial files: http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm verify that it works, then incrementally modify it to your rec-lig system. Scott From taylord at hsc.edu Sat Nov 7 10:40:30 2009 From: taylord at hsc.edu (David Taylor) Date: Sat, 7 Nov 2009 13:40:30 -0500 Subject: [Dock-fans] grid problem Message-ID: *So I've gotten everything together, and I've attempted to run both rigid and flex programs, but I keep getting this problem:* INPUT: molecular at molecular-desktop:~$ /home/molecular/Desktop/dock6/bin/dock6 -i rigid.in -o rigid.out OUTPUT: terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted *And in the rigid.out file I get this:* -------------------------------------- DOCK v6.2 Released March 2008 Copyright UCSF -------------------------------------- Molecule Library Input Parameters ------------------------------------------------------------------------------------------ ligand_atom_file ./1LAH_charged2.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol no Orient Ligand Parameters ------------------------------------------------------------------------------------------ orient_ligand yes automated_matching yes receptor_site_file ./selected_spheres.sph max_orientations 1000 critical_points no chemical_matching no use_ligand_spheres 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 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 Parameters ------------------------------------------------------------------------------------------ dock3.5_score_secondary no Continuous Energy Score Parameters ------------------------------------------------------------------------------------------ continuous_score_secondary no Zou GB/SA Score Parameters ------------------------------------------------------------------------------------------ gbsa_zou_score_secondary no Hawkins GB/SA Score Parameters ------------------------------------------------------------------------------------------ gbsa_hawkins_score_secondary no Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_secondary no Warning: No secondary scoring function selected. Simplex Minimization Parameters ------------------------------------------------------------------------------------------ minimize_ligand yes 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_random_seed 0 Atom Typing Parameters ------------------------------------------------------------------------------------------ atom_model all vdw_defn_file vdw_AMBER_parm99.defn flex_defn_file flex.defn flex_drive_file flex_drive.tbl Molecule Library Output Parameters ------------------------------------------------------------------------------------------ ligand_outfile_prefix output write_orientations no num_scored_conformers 10 write_conformations no cluster_conformations yes cluster_rmsd_threshold 2.0 rank_ligands no ------------------------------------------------------------------------------------------ Initializing Library File Routines... Initializing Orienting Routines... Initializing Grid Score Routines... Reading the energy grid from grid.nrg Error: memory exhausted! If this occurs during grid reading then a likely cause is a grid that is too large. Some machines have a very restrictive policy on allocating available resources: For Unix platforms increase the datasize, stacksize, and memoryuse using the limit, ulimit, or unlimit commands; use trial and error to find the apt one of these commands. *So yeah, that's the end of the output. I know this machine has run this program before, so I must be doing something wrong. I've also tried to increase stack size and other such things, but that didn't work too well for me either. Any ideas? Is my input put in wrong so that the computer is doing a lot of extra work or something?* *Thanks* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20091107/0df87f32/attachment.html From taylord at hsc.edu Sat Nov 7 12:08:50 2009 From: taylord at hsc.edu (David Taylor) Date: Sat, 7 Nov 2009 15:08:50 -0500 Subject: [Dock-fans] grid problem In-Reply-To: References: Message-ID: Sorry, I just figured it out. It was an input problem! Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20091107/8f97683d/attachment.html From cpsosa at msi.umn.edu Mon Nov 9 11:27:55 2009 From: cpsosa at msi.umn.edu (Carlos P Sosa) Date: Mon, 9 Nov 2009 13:27:55 -0600 (CST) Subject: [Dock-fans] Ligands with As Message-ID: <7c9f016de9bead9ad0cb66381d44175e.squirrel@www.msi.umn.edu> Hello, Does anybody know if it is possible to dock with dock6.3 ligands that have As? Thanks, From taylord at hsc.edu Tue Nov 10 11:35:11 2009 From: taylord at hsc.edu (David Taylor) Date: Tue, 10 Nov 2009 14:35:11 -0500 Subject: [Dock-fans] grid problem In-Reply-To: References: Message-ID: A couple of quick questions: 1) Do you know where I can find an interpretation of the grid score, vdw, etc? I have the answer now, I just don't know what it means. I've looked in the DOCK guide and I really didn't found anything that helps me out a lot... 2) How did you get the pictures of the molecule? Did you just snag them off the internet or did you take a screenshot of Chimera or what? So I think things are going rather well. I have my presentation at the end of this week and I think I have all the problems ironed out of the system. I'll start running a full test on my unknown next week and hopefully have it all done before the end of the semester! Thanks, --David Taylor On Sat, Nov 7, 2009 at 3:08 PM, David Taylor wrote: > Sorry, I just figured it out. It was an input problem! > > Thanks! > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20091110/e88d223a/attachment.html From sbrozell at rci.rutgers.edu Wed Nov 11 18:31:11 2009 From: sbrozell at rci.rutgers.edu (Scott Brozell) Date: Wed, 11 Nov 2009 21:31:11 -0500 Subject: [Dock-fans] grid problem In-Reply-To: References: Message-ID: <20091112023111.GL5327@casegroup.rutgers.edu> Hi, On Tue, Nov 10, 2009 at 02:35:11PM -0500, David Taylor wrote: > A couple of quick questions: > > 1) Do you know where I can find an interpretation of the grid score, vdw, > etc? I have the answer now, I just don't know what it means. I've looked in > the DOCK guide and I really didn't found anything that helps me out a lot... http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#whatisascore http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#GridEnergyScoring > 2) How did you get the pictures of the molecule? Did you just snag them off > the internet or did you take a screenshot of Chimera or what? It is quite cpmmon to take screenshots of Chimera. Scott From sbrozell at rci.rutgers.edu Wed Nov 11 18:55:16 2009 From: sbrozell at rci.rutgers.edu (Scott Brozell) Date: Wed, 11 Nov 2009 21:55:16 -0500 Subject: [Dock-fans] Ligands with As In-Reply-To: <7c9f016de9bead9ad0cb66381d44175e.squirrel@www.msi.umn.edu> References: <7c9f016de9bead9ad0cb66381d44175e.squirrel@www.msi.umn.edu> Message-ID: <20091112025516.GN5327@casegroup.rutgers.edu> Hi, On Mon, Nov 09, 2009 at 01:27:55PM -0600, Carlos P Sosa wrote: > > Does anybody know if it is possible to dock with dock6.3 ligands that have > As? There are no parameters for arsenic. The threshold for decent parameters for the basic DOCK scores is low; so it should be straightforward to get and add them to eg vdw_AMBER_parm99.defn. If you are planning sophisticated modeling starting with Amber Score then the threshold could be a lot higher. I think i heard that there will be progress in the 'novel atom' area in a near future antechamber. Scott From rjajra at gmail.com Fri Nov 13 07:23:24 2009 From: rjajra at gmail.com (Rameswer Lal Jajra) Date: Fri, 13 Nov 2009 20:53:24 +0530 Subject: [Dock-fans] How to use autodock Message-ID: <9012f0410911130723g4c8f397ep5ff897ca5b766f52@mail.gmail.com> Hello all, I am a new user on autodock, I dont know how to use bulk of ligands for docking in auto dock in single step. Is there any way by which I dont have to do auto-docking individually. I f anyone know plz help me. Thanks. -Rameswer lal -- Rameswer lal jajra 4th year Undergraduate Student, Department of Chemistry, IIT Bombay,Powai Mumbai 400076, India. Mobile: +91-9833173938 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20091113/456d7f78/attachment.html From reau_05 at yahoo.com Tue Nov 17 15:31:32 2009 From: reau_05 at yahoo.com (ethel urzo) Date: Tue, 17 Nov 2009 15:31:32 -0800 (PST) Subject: [Dock-fans] inquiry on Dock 6.2 Message-ID: <47913.32431.qm@web52108.mail.re2.yahoo.com> Hi! May I know how can I run DOCK 6.2 so that it would give 10 results (interaction energies)? is there any parameter in the DOCK synonymous to "number of runs/trials" which is adjustable? Or I have to repeat the whole process 10 times just to obtain 10 results? I am working with my undergraduate thesis and my adviser requires me 10 data for each ligand and then I'll get the mean.. Thank You. Ethel Urzo Get your preferred Email name! Now you can @ymail.com and @rocketmail.com. http://mail.promotions.yahoo.com/newdomains/aa/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20091117/969ca81e/attachment.html From tbalius at aol.com Tue Nov 17 17:01:34 2009 From: tbalius at aol.com (Trent Balius) Date: Tue, 17 Nov 2009 20:01:34 -0500 Subject: [Dock-fans] inquiry on Dock 6.2 In-Reply-To: <47913.32431.qm@web52108.mail.re2.yahoo.com> References: <47913.32431.qm@web52108.mail.re2.yahoo.com> Message-ID: <8CC3601CEE320A3-537C-3C31@webmail-d058.sysops.aol.com> Hi Ethel, The parameter you should change is the following: num_scored_conformers 10 Dock generates the same answers (for the same binary, on the same platform, and the same input file); so, rerunning dock will not help. Note the cluster heads are diverse poses. You may wish to turn clustering off. see the manual for http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFileOutput Hope this helps, Trent E. Balius Graduate Student, Rizzo Group Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 -----Original Message----- From: ethel urzo To: dock-fans at docking.org Sent: Tue, Nov 17, 2009 6:31 pm Subject: [Dock-fans] inquiry on Dock 6.2 Hi! May I know how can I run DOCK 6.2 so that it would give 10 results (interaction energies)? is there any parameter in the DOCK synonymous to "number of runs/trials" which is adjustable? Or I have to repeat the whole process 10 times just to obtain 10 results? I am working with my undergraduate thesis and my adviser requires me 10 data for each ligand and then I'll get the mean.. Thank You. Ethel Urzo Get your preferred Email name! Now you can @ymail.com and @rocketmail.com. _______________________________________________ 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... 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