From loraine.brillet at cea.fr Thu Aug 2 02:12:47 2007 From: loraine.brillet at cea.fr (BRILLET Loraine 216515) Date: Thu, 2 Aug 2007 11:12:47 +0200 Subject: [Dock-fans] RMSD calculation Message-ID: <7E82589CA662294BB063FBCD85928FF9888054@TOKYO.intra.cea.fr> Dear all, I usually use VMD to calculate RMSD between docking pose and crystallized pose. But this program uses the atom numbering given in input mol2 or pdb file to align the 2 molecules or to calculate the RMSD. So, it doesn't work properly if the atom numbering is not the same in the 2 files. I haven't manage yet to overcome this problem. I welcome any suggestion. Does anyone know if one (free) RMSD calculator exists, which uses sub-structural search to align ligands and calculate RMSD? Thanks for all the suggestions you could give me. Regards, Loraine -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070802/d16324f2/attachment.html From ksvinaykumar at gmail.com Thu Aug 2 07:16:42 2007 From: ksvinaykumar at gmail.com (Vinay Kumar) Date: Thu, 2 Aug 2007 19:46:42 +0530 Subject: [Dock-fans] Fe parameters Message-ID: Hello all, I am modelling a protein with protoporphyrin ring containing Fe. Could anyone please suggest the parameters that i need to include to get accurate docking results. With regards, Vinay -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070802/65d1a639/attachment.html From jji at cgl.ucsf.edu Thu Aug 2 10:47:55 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Thu, 02 Aug 2007 10:47:55 -0700 Subject: [Dock-fans] Fe parameters In-Reply-To: References: Message-ID: <46B218CB.3040001@cgl.ucsf.edu> Hi Vinay If this is a P450 or NOS, for example, and the ligand binding is either driven by electronics at the Fe or the ligand does not bind to the heme at all, then docking will not be much use, unless you are using a docking program that can account for electronics. Our Biochemistry paper may be of some interest regarding the use of docking to metalloenzymes. Irwin JJ, Raushel FM, Shoichet BK, "Virtual screening against metalloenzymes for inhibitors and substrates.", Biochemistry, 2005, 44(37),12316-28. DOI . Good luck! John Vinay Kumar wrote: > Hello all, > I am modelling a protein with protoporphyrin ring containing Fe. Could > anyone please suggest the parameters that i need to include to get > accurate docking results. > > With regards, > Vinay > ------------------------------------------------------------------------ > > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fan > From jji at cgl.ucsf.edu Thu Aug 2 11:09:15 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Thu, 02 Aug 2007 11:09:15 -0700 Subject: [Dock-fans] RMSD calculation In-Reply-To: <7E82589CA662294BB063FBCD85928FF9888054@TOKYO.intra.cea.fr> References: <7E82589CA662294BB063FBCD85928FF9888054@TOKYO.intra.cea.fr> Message-ID: <46B21DCB.6000208@cgl.ucsf.edu> Hi Loraine I believe this feature is available as "subtan" (shape Tanimoto) in the ROCS package and the shape toolkit from OpenEye. I am sure there are other programs that do this as well. Good luck. John BRILLET Loraine 216515 wrote: > > Dear all, > > > > I usually use VMD to calculate RMSD between docking pose and > crystallized pose. But this program uses the atom numbering given in > input mol2 or pdb file to align the 2 molecules or to calculate the > RMSD. So, it doesn?t work properly if the atom numbering is not the > same in the 2 files. I haven?t manage yet to overcome this problem. > > > > I welcome any suggestion. > > > > Does anyone know if one (free) RMSD calculator exists, which uses > sub-structural search to align ligands and calculate RMSD? > > > > Thanks for all the suggestions you could give me. > > > > Regards, > > > > Loraine > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > From sbrozell at scripps.edu Thu Aug 2 17:29:39 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Thu, 2 Aug 2007 17:29:39 -0700 Subject: [Dock-fans] bugfix.1 Message-ID: Hi, Ensure all cliques are examined as orients including the last one. See also http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-March/000933.html ********>Bugfix 1: Author: Demetri Moustakas and Scott Brozell Date: posted on dock-fans on March 5, 2007; reported on January 31, 2007 Program: dock Description: for ligand orienting the last clique was not being used. This bug was introduced before version 5.2.0. Fix: make the following changes to the files src/dock/orient.cpp and install/test/ligand_orienting/orient2.dockout.save ------------------------------------------------------------------------- *** src/dock/orient.cpp 15 Dec 2006 01:34:40 -0000 1.11.2.2 --- src/dock/orient.cpp 1 Feb 2007 06:10:04 -0000 *************** *** 1487,1494 **** current_clique++; if ((current_clique == max_orients) ! || (current_clique == cliques.size() - 1)) last_orient_flag = true; else{ last_orient_flag = false; --- 1493,1502 ---- current_clique++; + // DTM - ensure all cliques are examined as + // orients including the last one - 1/30/07 if ((current_clique == max_orients) ! || (current_clique == cliques.size())) last_orient_flag = true; else{ last_orient_flag = false; =================================================================== *** install/test/ligand_orienting/orient2.dockout.save 15 Dec 2006 01:34:21 -0000 1.5.2.1 --- install/test/ligand_orienting/orient2.dockout.save 27 Jul 2007 00:39:30 -0000 *************** *** 67,74 **** Elapsed time for docking: 0 seconds Anchors: 1 ! Orientations: 35 ! Conformations: 35 --- 67,74 ---- Elapsed time for docking: 0 seconds Anchors: 1 ! Orientations: 36 ! Conformations: 36 -------------------------------------------------------------------------- Workaround: none. From sbrozell at scripps.edu Thu Aug 2 17:32:03 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Thu, 2 Aug 2007 17:32:03 -0700 Subject: [Dock-fans] bugfix.3 Message-ID: Hi, Incorrect electrostatics with gbsa_hawkins_score_cont_vdw_and_es = yes. ********>Bugfix 3: Author: Sudipto Mukherjee and Scott Brozell Date: July 26, 2007 Program: dock Description: for Hawkins GB/SA score with gbsa_hawkins_score_cont_vdw_and_es = yes the electrostatic component was being calculated as q1*q2/r^2 instead of q1*q2/r. Fix: make the following changes to the files src/dock/score_solvent.cpp install/test/hawkins_gbsa_score/hawkins_gbsa1.dockout.save and install/test/hawkins_gbsa_score/hawkins_gbsa1_scored.mol2.save ------------------------------------------------------------------------- *** src/dock/score_solvent.cpp 15 Dec 2006 01:34:41 -0000 1.17.2.2 --- src/dock/score_solvent.cpp 27 Jul 2007 01:09:22 -0000 *************** *** 1773,1779 **** pow(dist, vdw_score.att_exp)); es_component += ((332 * receptor.charges[i] * ligand.charges[j]) / ! (pow(dist, 2))); } } } --- 1773,1781 ---- pow(dist, vdw_score.att_exp)); es_component += ((332 * receptor.charges[i] * ligand.charges[j]) / ! dist); ! // for gbsa, gas phase electrostatics should be used ! // as in q1*q2/r not q1*q2/r^2 } } } =================================================================== *** install/test/hawkins_gbsa_score/hawkins_gbsa1.dockout.save 15 Dec 2006 01:34:20 -0000 1.4.2.1 --- install/test/hawkins_gbsa_score/hawkins_gbsa1.dockout.save 27 Jul 2007 01:35:44 -0000 *************** *** 103,120 **** ----------------------------------- Molecule: C1 ! Elapsed time for docking: 36 seconds Anchors: 1 Orientations: 1 Conformations: 1 ! GB/SA Score: -52.142647 vdw: -53.120110 ! es: -10.411127 gb: 16.258278 sa: -4.869689 1 Molecules Processed ! Total elapsed time: 74 seconds --- 103,120 ---- ----------------------------------- Molecule: C1 ! Elapsed time for docking: 24 seconds Anchors: 1 Orientations: 1 Conformations: 1 ! GB/SA Score: -58.245907 vdw: -53.120110 ! es: -16.514385 gb: 16.258278 sa: -4.869689 1 Molecules Processed ! Total elapsed time: 50 seconds =================================================================== *** install/test/hawkins_gbsa_score/hawkins_gbsa1_scored.mol2.save 15 Dec 2006 01:34:20 -0000 1.1.2.1 --- install/test/hawkins_gbsa_score/hawkins_gbsa1_scored.mol2.save 27 Jul 2007 01:35:44 -0000 *************** *** 1,8 **** ########## Name: C1 ! ########## GB/SA Score: -52.142647 ########## vdw: -53.120110 ! ########## es: -10.411127 ########## gb: 16.258278 ########## sa: -4.869689 --- 1,8 ---- ########## Name: C1 ! ########## GB/SA Score: -58.245907 ########## vdw: -53.120110 ! ########## es: -16.514385 ########## gb: 16.258278 ########## sa: -4.869689 -------------------------------------------------------------------------- Workaround: none. From sbrozell at scripps.edu Thu Aug 2 17:35:18 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Thu, 2 Aug 2007 17:35:18 -0700 Subject: [Dock-fans] bugfix.4 Message-ID: Hi, Improved error reporting for conformation writing in parallel dock. For the report of this bug see http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-June/001076.html ********>Bugfix 4: Author: Scott Brozell and Terry Lang, reported by Grzegorz Popowicz Date: July 27, 2007 Program: dock6.mpi Description: parallel dock should emit an error message when num_primary_scored_conformers_rescored > 1, num_secondary_scored_conformers_written > 1, or num_scored_conformers_written > 1 otherwise performance can be substantially degraded. Fix: make the following changes to the files src/dock/src/dock/orient.cpp ------------------------------------------------------------------------- *** library_file.cpp 15 Dec 2006 01:34:39 -0000 1.13.2.8 --- library_file.cpp 27 Jul 2007 21:50:26 -0000 *************** *** 603,609 **** exit(0); } if (num_scored_poses > 1) { ! write_conformers = true; cluster_ranked_poses = (parm.query_param("cluster_primary_conformations", "yes", "yes no") == "yes") ? true : false; --- 603,617 ---- exit(0); } if (num_scored_poses > 1) { ! if ( ! USE_MPI ) ! write_conformers = true; ! else { ! cout << ! "ERROR: DOCK cannot write conformations while running in parallel." ! << endl; ! finalize_mpi(); ! exit(0); ! } cluster_ranked_poses = (parm.query_param("cluster_primary_conformations", "yes", "yes no") == "yes") ? true : false; *************** *** 624,631 **** if(!rank_secondary_ligands) { num_secondary_scored_poses = atoi(parm.query_param("num_secondary_scored_conformers_written", "1").c_str()); ! if(num_secondary_scored_poses > 1) ! write_secondary_conformers = true; if(num_secondary_scored_poses > num_scored_poses){ cout << "ERROR: Number of secondary poses written cannot exceed number of primary "; cout << "poses rescored. Program will terminate." << endl; --- 632,648 ---- if(!rank_secondary_ligands) { num_secondary_scored_poses = atoi(parm.query_param("num_secondary_scored_conformers_written", "1").c_str()); ! if(num_secondary_scored_poses > 1) { ! if ( ! USE_MPI ) ! write_secondary_conformers = true; ! else { ! cout << ! "ERROR: DOCK cannot write conformations while running in parallel." ! << endl; ! finalize_mpi(); ! exit(0); ! } ! } if(num_secondary_scored_poses > num_scored_poses){ cout << "ERROR: Number of secondary poses written cannot exceed number of primary "; cout << "poses rescored. Program will terminate." << endl; *************** *** 650,656 **** exit(0); } if (num_scored_poses > 1) { ! write_conformers = true; cluster_ranked_poses = (parm.query_param("cluster_conformations", "yes", "yes no") == "yes") ? true : false; --- 667,681 ---- exit(0); } if (num_scored_poses > 1) { ! if ( ! USE_MPI ) ! write_conformers = true; ! else { ! cout << ! "ERROR: DOCK cannot write conformations while running in parallel." ! << endl; ! finalize_mpi(); ! exit(0); ! } cluster_ranked_poses = (parm.query_param("cluster_conformations", "yes", "yes no") == "yes") ? true : false; -------------------------------------------------------------------------- Workaround: none. From ksvinaykumar at gmail.com Fri Aug 3 07:12:21 2007 From: ksvinaykumar at gmail.com (Vinay Kumar) Date: Fri, 3 Aug 2007 19:42:21 +0530 Subject: [Dock-fans] sphgen error Message-ID: Hi all, This is the error message that i get on running sphgen. could someone explain this. $ sphgen fmt: read unexpected character apparent state: internal I/O last format: (A3,I3,A1,2X,A4,1X,F7.3,2F9.3,1X,A3,7X,3F7.3) lately reading sequential formatted internal IO Aborted Also, the tutorial says that sphgen can handle 9999 spheres only, how do i selectively select residues and generate spheres ?? further i would like to know which version of chimera was used for in the tutorial files?? since i do not find the same submenus on the chimera i have?? Regards, Vinay -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070803/86a851b9/attachment.html From pett at cgl.ucsf.edu Fri Aug 3 19:15:21 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 3 Aug 2007 19:15:21 -0700 Subject: [Dock-fans] RMSD calculation Message-ID: <250C248D-3C4C-4528-8B21-69741D99AA25@cgl.ucsf.edu> > I usually use VMD to calculate RMSD between docking pose and > crystallized pose. But this program uses the atom numbering given in > input mol2 or pdb file to align the 2 molecules or to calculate the > RMSD. So, it doesn't work properly if the atom numbering is not the > same > in the 2 files. I haven't manage yet to overcome this problem. > > I welcome any suggestion. > > Does anyone know if one (free) RMSD calculator exists, which uses > sub-structural search to align ligands and calculate RMSD? Chimera can't do substructure matching, but if the atom names in the two files correspond then Chimera will match them correctly regardless of the order in the file (use the "match" command). I hope this helps. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu From pett at cgl.ucsf.edu Fri Aug 3 19:23:56 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 3 Aug 2007 19:23:56 -0700 Subject: [Dock-fans] sphgen error Message-ID: > further i would like to > know which version of chimera was used for in the tutorial files?? > since i > do not find the same submenus on the chimera i have?? My best guess is version 1.2304. Nonetheless, I recommend you use the latest version of Chimera despite the small differences in the menus since the latest release is always for the most part an improvement on previous versions. I would only go back to an earlier version if there was something specific I knew was broken in the latest version that worked earlier, and I don't think that's the case here. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu From popowicz at biochem.mpg.de Mon Aug 6 02:39:21 2007 From: popowicz at biochem.mpg.de (Grzegorz Popowicz) Date: Mon, 6 Aug 2007 11:39:21 +0200 Subject: [Dock-fans] Anchor size and clashes elimination In-Reply-To: References: Message-ID: <200708061139.22094.popowicz@biochem.mpg.de> Hi all! 1. The default size of an anchor in DOCK is 40 atoms this generates quite big fragments as for beginning of docking (at least 480Da). I have tried smaller anchors (8 atoms) with good results. Are there any rules governing selection of anchor size? 2. Dock run with use_clash_overlap=no generates solutions with terrible clashes (of course), however the predictions of known ligands binding are very good in my case. With use_clash_overlap=yes and clash_overlap=0.5 (BTW. What does percent of overlap mean?) there are no clushes but known ligands are badly docked and scored much much worse than without clashes filter. Is there any resonable explanation to this fact? Gregor From andreyvoronkov at yandex.ru Tue Aug 7 12:45:54 2007 From: andreyvoronkov at yandex.ru (Voronkov Andrew) Date: Tue, 07 Aug 2007 23:45:54 +0400 Subject: [Dock-fans] which drugs were elaborated with Dock 6.0 software? Message-ID: <127871186515954@webmail21.yandex.ru> Dear Dock administration, Do you have data about drugs or prodrugs which were elaborated with Dock software? Sincerely yours, Andrew From jji at cgl.ucsf.edu Tue Aug 7 13:36:38 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Tue, 07 Aug 2007 13:36:38 -0700 Subject: [Dock-fans] which drugs were elaborated with Dock 6.0 software? In-Reply-To: <127871186515954@webmail21.yandex.ru> References: <127871186515954@webmail21.yandex.ru> Message-ID: <46B8D7D6.1030605@cgl.ucsf.edu> Hi Andrew I do not have such a list at hand. One reason is that the trip from initial hit that you get from DOCK to a marketed drug is an expensive process that takes many years and generally involves many people and technologies. There are however dozens of compounds on the market or in clinical trials that were discovered by structure-guided drug design techniques including DOCK. I recall seeing such a list in Dec 2003 at currentdrugdiscovery.com (I have it on my wall!). There will be more recent versions of this table around I am sure. Hope this is of some use. John Voronkov Andrew wrote: > Dear Dock administration, > Do you have data about drugs or prodrugs which were elaborated with Dock software? > > Sincerely yours, > Andrew > _______________________________________________ > Dock-fans mailing list > Dock-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > From axkiely at gmail.com Tue Aug 7 17:13:36 2007 From: axkiely at gmail.com (Aidan Kiely) Date: Wed, 8 Aug 2007 12:13:36 +1200 Subject: [Dock-fans] Dock6: Command not found Message-ID: Hi Dock Fans, This may seem a daft question, but Im not sure where to turn. Ive RTFM, browsed the mailing list archives and searched the 'net but it seems no-one has had this problem. Ive attempted to install Dock6.1 on a windows machine running the latest version of Cygwin (full install). I follow the instructions for installation and it seems to work fine. Running the tests gets some "possible failures", but looking at the .dif files it looks as though they are small numerical differences ie i dont think they are major. However, when i attempt to run dock from a Cyqwin bash window (on tutorial files) using the command dock6 -i rigid.in [-o rigid.out] it gives me the error "bash dock6: command not found". Can anyone point in me in the right direction? Kind Regards, Aidan Kiely University of Auckland -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070808/b62adcda/attachment.html From sudmukh at yahoo.com Tue Aug 7 17:24:10 2007 From: sudmukh at yahoo.com (Sudipto Mukherjee) Date: Tue, 7 Aug 2007 17:24:10 -0700 (PDT) Subject: [Dock-fans] Dock6: Command not found Message-ID: <312343.96600.qm@web36703.mail.mud.yahoo.com> Aidan, This is because the dock6 binary is not in your current path. Add the dock6/bin directory to your path (doing so in your .bash_profile or .bashrc is a good idea) and you should be able to run dock without any problems. Otherwise, simply provide the full path when you are executing dock. For example, /home/aidan/dock6/bin/dock6 -i rigid.in Regards Sudipto Mukherjee Graduate Student, Robert C. Rizzo Lab Dept. of Applied Math & Statistics, Stony Brook University ----- Original Message ---- From: Aidan Kiely To: dock-fans at docking.org Sent: Tuesday, August 7, 2007 8:13:36 PM Subject: [Dock-fans] Dock6: Command not found Hi Dock Fans, This may seem a daft question, but Im not sure where to turn. Ive RTFM, browsed the mailing list archives and searched the 'net but it seems no-one has had this problem. Ive attempted to install Dock6.1 on a windows machine running the latest version of Cygwin (full install). I follow the instructions for installation and it seems to work fine. Running the tests gets some "possible failures", but looking at the .dif files it looks as though they are small numerical differences ie i dont think they are major. However, when i attempt to run dock from a Cyqwin bash window (on tutorial files) using the command dock6 -i rigid.in [-o rigid.out] it gives me the error "bash dock6: command not found". Can anyone point in me in the right direction? Kind Regards, Aidan Kiely University of Auckland ____________________________________________________________________________________Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV. http://tv.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070807/ee6d7e20/attachment-0001.html From sudmukh at yahoo.com Tue Aug 7 17:45:35 2007 From: sudmukh at yahoo.com (Sudipto Mukherjee) Date: Tue, 7 Aug 2007 17:45:35 -0700 (PDT) Subject: [Dock-fans] Anchor size and clashes elimination Message-ID: <261159.6501.qm@web36707.mail.mud.yahoo.com> Grzegorz, Min Anchor size: The default size of 40 atoms will cause Dock to select the largest anchor only for most molecules. Using a smaller anchor size rapidly increases the execution time though. min_anchor_size of 6 means the anchor can be as small as a single benzene ring. This parameter is somewhat analogous to the multiple_anchors parameter present in DOCK 4. Using multiple anchors can improve sampling in some cases, but mostly results in sampling similar conformers multiple times. Also, I would recommend using clustering when using a small min_anchor_size to prune the number of similar conformers sampled. Clash_overlap: DOCK computes clash overlap with the following formula: if ( distance(atom_A, atom_B) < clash_overlap *( radius_atom_A + radius_atom_B ) ) assume there is a clash See the segment_clash_check() function in conf_gen.ccp for details. Regards Sudipto Mukherjee Graduate Student, Robert C. Rizzo Lab Dept. of Applied Math & Statistics, Stony Brook University ----- Original Message ---- From: Grzegorz Popowicz To: dock-fans at docking.org Sent: Monday, August 6, 2007 5:39:21 AM Subject: [Dock-fans] Anchor size and clashes elimination Hi all! 1. The default size of an anchor in DOCK is 40 atoms this generates quite big fragments as for beginning of docking (at least 480Da). I have tried smaller anchors (8 atoms) with good results. Are there any rules governing selection of anchor size? 2. Dock run with use_clash_overlap=no generates solutions with terrible clashes (of course), however the predictions of known ligands binding are very good in my case. With use_clash_overlap=yes and clash_overlap=0.5 (BTW. What does percent of overlap mean?) there are no clushes but known ligands are badly docked and scored much much worse than without clashes filter. Is there any resonable explanation to this fact? Gregor _______________________________________________ Dock-fans mailing list Dock-fans at docking.org http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans ____________________________________________________________________________________ Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center. http://autos.yahoo.com/green_center/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070807/5b825a8d/attachment.html From hshallal at gmail.com Thu Aug 9 12:59:54 2007 From: hshallal at gmail.com (hassan shallal) Date: Thu, 9 Aug 2007 12:59:54 -0700 Subject: [Dock-fans] A huge difference in results Message-ID: <23d18a200708091259x77d09ed5nd49d6f5d520de466@mail.gmail.com> Dear Dock users, I am a beginner of using dock. I just have finished my first dock experiment using the tutorials posted in http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm. I compared the results I obtained in My experiment (attached are two files, My_flex_scored.mol2 and My_rigid_scored.mol2) and the results posted in the tutorial (attached are other two files, (Tutorial_flex_scored.mol2 and Tutorial_rigid_scored.mol2). I found that there is a good agreement between the obtained and the posted VDW results. However, a huge difference within the range of 8-9 was observed in both the case of grid score and electrostatic interaction. I actually have two questions: The first: why this difference happened? is there a problem in my compilers that has led to this difference? if yes, how can I solve it? The second: how can I calculate the free energy of binding (delta G) by using the above values? I do appreciate any response to my issue Great Regards Hassan Shallal University of the Pacific California -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070809/b6ac5d87/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: My_flex_scored.mol2 Type: application/octet-stream Size: 2357 bytes Desc: not available Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070809/b6ac5d87/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: My_rigid_scored.mol2 Type: application/octet-stream Size: 2357 bytes Desc: not available Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070809/b6ac5d87/attachment-0001.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: Tutorial_flex_scored.mol2 Type: application/octet-stream Size: 2366 bytes Desc: not available Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070809/b6ac5d87/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: Tutorial_rigid_scored.mol2 Type: application/octet-stream Size: 2366 bytes Desc: not available Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070809/b6ac5d87/attachment-0003.obj From sbrozell at scripps.edu Thu Aug 9 18:56:33 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Thu, 9 Aug 2007 18:56:33 -0700 Subject: [Dock-fans] Reading the energy grid from ../3_grid/grid.nrg In-Reply-To: References: Message-ID: Hi, Please send questions to dock-fans: http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > > dock6 -i dock.in [-o dock.out] > > *** glibc detected *** malloc(): memory corruption (fast): Please provide all the input files and I'll try to reproduce the failure. Scott On Wed, 8 Aug 2007, Julie Kneller wrote: > Thanks for your help so far. I have rigid docking working now (using > smaller ligand and receptor files) but I still get a segmentation fault > using the flexible docking using identical input files. Can you think > of anything that could be causing this? --Julie > > -----Original Message----- > From: Terry Lang > Sent: Wednesday, August 08, 2007 3:36 PM > Subject: Re: Question: Reading the energy grid from ../3_grid/grid.nrg > > Dear Julie, > > There appears to be some kind of memory issue. Since all your > tests passed, there is probably something wrong with your personal > system. A couple of things to check: > > 1) Open your ligand in a molecular viewer. Does it look reasonable? > Are bonds missing? > 2) How big is your grid? > 3) Are all of your spheres inside the grid box? > > If you continue to have problems, please send your files along so we can > take a better look. > > Sincerely, > Terry > > > Julie Kneller wrote: > > Can you help me? Everything has worked perfectly up until this final > > point, --Julie > > > > > > when trying rigid docking using > > > > dock6 -i rigid.in [-o rigid.out] > > > > I get a sementation fault. The last line of rigid.out is "Reading the > > > energy grid from ../3_grid/grid.nrg". The last line of grid.out is > > "Finished calculation." > > > > > > when trying flex docking using > > > > dock6 -i dock.in [-o dock.out] > > > > I get the following message: > > > > *** glibc detected *** malloc(): memory corruption (fast): > > 0x00000000008d1150 *** > > Aborted > > From sbrozell at scripps.edu Fri Aug 10 12:42:04 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Fri, 10 Aug 2007 12:42:04 -0700 Subject: [Dock-fans] A huge difference in results In-Reply-To: <23d18a200708091259x77d09ed5nd49d6f5d520de466@mail.gmail.com> References: <23d18a200708091259x77d09ed5nd49d6f5d520de466@mail.gmail.com> Message-ID: Hi, On Thu, 9 Aug 2007, hassan shallal wrote: > I am a beginner of using dock. I just have finished my first dock experiment > using the tutorials posted in > http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm. > > I compared the results I obtained in My experiment (attached are two files, > My_flex_scored.mol2 and My_rigid_scored.mol2) and the results posted in the > tutorial (attached are other two files, (Tutorial_flex_scored.mol2 and > Tutorial_rigid_scored.mol2). > > I found that there is a good agreement between the obtained and the posted > VDW results. However, a huge difference within the range of 8-9 was observed > in both the case of grid score and electrostatic interaction. ########## Name: 1ABE.pdb ########## Grid Score: -41.291992 ########## vdw: -21.404663 ########## es: -19.887329 ########## Name: 1ABE.pdb ########## Grid Score: -36.147507 ########## vdw: -21.315907 ########## es: -14.831600 6 O1 14.6521 57.3674 56.3454 O.3 1 ARA307 -0.5790 ########## Name: UNNAMED ########## Grid Score: -33.120888 ########## vdw: -22.171465 ########## es: -10.949423 ########## Name: UNNAMED ########## Grid Score: -28.794184 ########## vdw: -22.208521 ########## es: -6.585662 19 O1 14.5687 57.5120 56.4257 O.3 1 ARA1 -0.3649 > I actually have two questions: > The first: why this difference happened? is there a problem in my compilers > that has led to this difference? if yes, how can I solve it? > The second: how can I calculate the free energy of binding (delta G) by > using the above values? Counting ?'s there are 4 questions: 1. The charges are significantly different for all the atoms. So the difference is likely due to Coulomb's law. 2. Unknown, but no evidence of that yet. Run the test suite to validate your installation. See http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Installation and the blurb at the end of that section for other sources of error. 3. This question does not exist yet. 4. One could approximate the binding energy as the score. http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OverviewoftheDOCKSuiteofPrograms But see previous posts for warnings: http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-March/000973.html Scott From axkiely at gmail.com Sun Aug 12 02:05:53 2007 From: axkiely at gmail.com (Aidan Kiely) Date: Sun, 12 Aug 2007 21:05:53 +1200 Subject: [Dock-fans] Showsphere errors? Message-ID: Hi Dock-Fans, I am having problems running the showsphere program on either my own experimental or the tutorial files. I get the following error in the only output file (showsphere.exe.stackdump) along with a number array: 5 [sig] showsphere 4016 c:\dock6\bin\showsphere.exe: *** fatal error - called with threadlist_ix -1 I can attach my make check and make test log files if required, but they are 40kb and 85 kb. I am running dock6.1 through cygwin and have no problems up until this point in the tutorial process. Any help would be appreciated. Kind Regards, Aidan Kiely -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070812/48e8ef1d/attachment.html From sbrozell at scripps.edu Sun Aug 19 10:21:28 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Sun, 19 Aug 2007 10:21:28 -0700 Subject: [Dock-fans] Showsphere errors? In-Reply-To: References: Message-ID: Hi, On Sun, 12 Aug 2007, Aidan Kiely wrote: > I am having problems running the showsphere program on either my own > experimental or the tutorial files. I get the following error in the only > output file (showsphere.exe.stackdump) along with a number array: > > 5 [sig] showsphere 4016 c:\dock6\bin\showsphere.exe: *** fatal error - > called with threadlist_ix -1 > > I can attach my make check and make test log files if required, but they are > 40kb and 85 kb. I am running dock6.1 through cygwin and have no problems up > until this point in the tutorial process. What happens when you run the sphere_generation test ? cd dock6/install/test/sphere_generation make clean make make check Scott From massiah at biochem.okstate.edu Thu Aug 23 09:28:15 2007 From: massiah at biochem.okstate.edu (michael massiah) Date: Thu, 23 Aug 2007 11:28:15 -0500 Subject: [Dock-fans] (no subject) Message-ID: Hi We are trying to use Dock6 to perform flexible docking but have been running into problem. We get the following error. Molecule: 19mer-1.pdb Elapsed time: 11 seconds ERROR: Could not complete growth. Confirm grid box is large enough to contain ligand and try increasing max_orients. We think the problem is with the sph file. we have an old sph file that works but any newly generated sph file does not. the difference in spheres between the old sph and new sph files are very very subtle in terms of their xyz coordinates and they cover the same area, when we superimposed the spheres. but no matter what we do, we can get newer sph files to work. Any suggestion. Mike From sbrozell at scripps.edu Tue Aug 28 08:39:31 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Tue, 28 Aug 2007 08:39:31 -0700 Subject: [Dock-fans] (no subject) In-Reply-To: References: Message-ID: Hi, On Thu, 23 Aug 2007, michael massiah wrote: > We are trying to use Dock6 to perform flexible docking but have been > running into problem. We get the following error. > > Molecule: 19mer-1.pdb > > Elapsed time: 11 seconds > > ERROR: Could not complete growth. > Confirm grid box is large enough to contain > ligand and try increasing max_orients. > > We think the problem is with the sph file. we have an old sph file > that works but any newly generated sph file does not. the difference > in spheres between the old sph and new sph files are very very subtle > in terms of their xyz coordinates and they cover the same area, when > we superimposed the spheres. but no matter what we do, we can get > newer sph files to work. Any suggestion. What are some other details of the old and new sphere files : commands to create them; apparently, the molecular surface file is the same; apparently, the sphere selection is the same; file sizes. Are you using a bump grid ? Scott From sbrozell at scripps.edu Tue Aug 28 09:17:39 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Tue, 28 Aug 2007 09:17:39 -0700 Subject: [Dock-fans] Error during installation In-Reply-To: <46D32549.6020109@blur.compbio.ucsf.edu> References: <46D32549.6020109@blur.compbio.ucsf.edu> Message-ID: Hi, On Mon, 27 Aug 2007, wrote: > I have few questions about the errors occurred > during the installation of dock6. Here are the messages. Are there normal or > is there anything I can fix? Thanks a lot and I really really appreciate it. > > Sincerely, > Byoung-Chul > > (1) sff.c:1614: warning: incompatible implicit declaration of built-in > function 'strdup' This is unusual, but probably is not a problem. Is your Mac powerbook OS X 10.4.10 a 32 or 64 bit machine ? What is the version of gcc ? The other types of warnings are normal. For a little explanation see http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-May/001029.html Scott > (2) In file included from /usr/include/c++/4.0.0/backward/strstream:51, > from sphere_selector.cpp:7: > /usr/include/c++/4.0.0/backward/backward_warning.h:32:2: warning: #warning > This file includes at least one deprecated or antiquated header. Please > consider using one of the 32 headers found in section 17.4.1.2 of the C++ > standard. Examples include substituting the header for the header > for C++ includes, or instead of the deprecated header > . To disable this warning use -Wno-deprecated. > > (3) pdb_sprntf.c:279: warning: incompatible implicit declaration of built-in > function 'strlen' > (4) residue.c:336: warning: passing argument 1 of 'AtomBondTo' from > incompatible pointer type > residue.c:336: warning: passing argument 2 of 'AtomBondTo' from incompatible > pointer type > residue.c:464: warning: passing argument 1 of 'BuildFixInternals' from > incompatible pointer typ > > (5) unitio.c: In function 'zUnitIOSaveAmberParmFormat': > unitio.c:4047: warning: passing argument 1 of 'SortByInteger' from > incompatible pointer type > unitio.c:4047: warning: passing argument 4 of 'SortByInteger' from > incompatible pointer type > unitio.c: In function 'zUnitIOSaveAmberParmFormat_old': > unitio.c:6055: warning: passing argument 1 of 'SortByInteger' from > incompatible pointer type > unitio.c:6055: warning: passing argument 4 of 'SortByInteger' from > incompatible pointer type > gcc -c -O2 -DSYSV graphUtil.c > graphUtil.c: In function 'GraphUtilFindAllSmallestRingsAndRingGroups': > graphUtil.c:675: warning: passing argument 1 of 'SortByInteger' from > incompatible pointer type > graphUtil.c:675: warning: passing argument 4 of 'SortByInteger' from > incompatible pointer type > gcc -c -O2 -DSYSV select.c > gcc -c -O2 -DSYSV amber.c > amber.c: In function 'uAmberReadUnitFromPrep': > amber.c:986: warning: passing argument 1 of 'SortByInteger' from > incompatible pointer type > amber.c:986: warning: passing argument 4 of 'SortByInteger' from > incompatible pointer type > gcc -c -O2 -DSYSV build.c > build.c: In function 'bBuildFlipChiralityFor': > build.c:1901: warning: passing argument 1 of 'SortByInteger' from > incompatible pointer type > build.c:1901: warning: passing argument 4 of 'SortByInteger' from > incompatible pointer type > build.c:1907: warning: passing argument 1 of 'GraphUtilFindAllSmallestRings' > from incompatible pointer type > build.c: In function 'BuildInternalsForSimpleRings': > build.c:2185: warning: passing argument 1 of > 'GraphUtilFindAllSmallestRingsAndRingGroups' from incompatible pointer type > > (6) model.c: In function 'zModelOrderAtoms': > model.c:497: warning: passing argument 1 of 'Sift' from incompatible pointer > type > gcc -c -O2 -DSYSV parmLib.c > gcc -c -O2 -DSYSV pdbFile.c > pdbFile.c: In function 'zPdbBuildCoordinatesForContainer': > pdbFile.c:1088: warning: passing argument 1 of 'BuildFixInternals' from > incompatible pointer type > pdbFile.c: In function 'zPdbAddAtom': > pdbFile.c:1207: warning: passing argument 1 of 'BuildInternalsForContainer' > from incompatible pointer type > pdbFile.c: In function 'writeTER': > pdbFile.c:1761: warning: initialization from incompatible pointer type > gcc -c -O2 -DSYSV tools.c > tools.c: In function 'iToolDistanceSearch': > tools.c:1643: warning: passing argument 1 of 'SortByDouble' from > incompatible pointer type > tools.c:1643: warning: passing argument 4 of 'SortByDouble' from > incompatible pointer type > tools.c: In function 'ToolOrientPrincipleAxisAlongCoordinateAxis': > tools.c:1714: warning: passing argument 2 of 'MathOpDiagonalize' from > incompatible pointer type > > (7) yacc: 6 shift/reduce conflicts. > (The warning 'conflicts: 6 shift/reduce' is normal) > > (8) commands.c: In function 'oCmd_impose': > commands.c:3835: warning: passing argument 1 of 'bBuildChangeInternalBond' > from incompatible pointer type > commands.c:3859: warning: passing argument 1 of 'bBuildChangeInternalAngle' > from incompatible pointer type > commands.c:3885: warning: passing argument 1 of > 'bBuildChangeInternalTorsion' from incompatible pointer type > > > On 8/15/07 3:39 PM, "John J. Irwin" wrote: > > > Hi - if it is correctly installed, then log out and log back in and type > > which g77 and it should tell you where it is. If it can't find it, then > > there is a problem. You can look in /usr/bin/g77 . If you find it there, > > then you need to add /usr/bin to your path. you can also do find / > > -name 'g77' to find where g77 lives, and then add that directory to > > your path. > > > > good luck. > > > > > > Byoung-Chul Lee wrote: > >> Dear John, > >> > >> I just got the g77 3.4 binary files for Mac. I think I installed the g77. > >> But still I got the same message that g77 is not found. Can you please let > >> me know how to make the g77 work for DOCK installation? Thanks a lot. > >> > >> Sincerely, > >> > >> Byoung-Chul > >> > >> > >> On 8/15/07 10:07 AM, "John J. Irwin" wrote: > >> > >> > >>> Hi Byoung-Chul > >>> > >>> You need to install g77. > >>> > >>> Good luck. > >>> > >>> John > >>> > >>> > >>> Byoung-Chul Lee wrote: > >>> > >>>> Dear whom it may concern, > >>>> > >>>> I am currently installing the Dock6 in my Mac powerbook OS X 10.4.10. > >>>> During > >>>> installation, I got the following error message at the end. > >>>> > >>>> make[2]: g77: Command not found > >>>> make[2]: *** [showbox.o] Error 127 > >>>> make[1]: *** [utils] Error 2 > >>>> make: *** [install] Error 2 > >>>> > >>>> Is this a serious error? Can you please let me know how I can fix the > >>>> problem? Thanks!!! From sbrozell at scripps.edu Tue Aug 28 17:21:03 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Tue, 28 Aug 2007 17:21:03 -0700 Subject: [Dock-fans] constrained docking Message-ID: Hi, Piotr Cieplak wrote: > I want to do constrained docking, e.g. keep some portion of the docked > molecules in the same place (could move slightly) while the other part > moves freely. For example - keep a single peptide bond or carboxy group > in place, while the rest of the molecule could float in space. Is it > possible to do something like that with DOCK6.0? > Thanks for any help with that. One general feature of Dock that might have been able to enable constrained docking: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#ManualSpecificationofNonrotatableBonds is not currently available: http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-April/000982.html Selecting parts of a molecule is possible with Amber score, but Amber score does not yet support full fledged docking. As an aside I recommend upgrading to dock 6.1: http://dock.compbio.ucsf.edu/DOCK_6/6.1/new_in_6.1.txt Scott From gongxingwen at 163.com Wed Aug 29 23:25:32 2007 From: gongxingwen at 163.com (gongxingwen) Date: Thu, 30 Aug 2007 14:25:32 +0800 (CST) Subject: [Dock-fans] How to continue when terminated unexpectedly Message-ID: <32984419.697091188455132356.JavaMail.coremail@bj163app61.163.com> Hi, I would like to know if I can continue the previous work (flex or amber dock) when it was terminated unexpectedly such as power failure. Any parameter has this function ? Thanks! Gong -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070830/5d0e69ea/attachment.html From sbrozell at scripps.edu Fri Aug 31 15:09:07 2007 From: sbrozell at scripps.edu (Scott Brozell) Date: Fri, 31 Aug 2007 15:09:07 -0700 Subject: [Dock-fans] How to continue when terminated unexpectedly In-Reply-To: <32984419.697091188455132356.JavaMail.coremail@bj163app61.163.com> References: <32984419.697091188455132356.JavaMail.coremail@bj163app61.163.com> Message-ID: Hi, On Thu, 30 Aug 2007, gongxingwen wrote: > Hi, I would like to know if I can continue the previous work (flex or amber dock) when it was terminated unexpectedly such as power failure. Any parameter has this function ? Thanks! Gong There is still no special restart option yet: http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-February/000577.html Generally, one examines the output files to determine what has been calculated and then modifies the new inputs accordingly. For Amber rescoring, only with the verbose option, dock6 -v ..., does dock emit enough information to in general determine what poses have been rescored. In particular, in the output ... ligand_atom_file FINAL_new_AM1BCC_conformers.amber_score.mol2 ... Reading the ligand FINAL_new_AM1BCC_conformers.2 input files. ... The 2 is the AMBER_SCORE_ID. This is determined from the order of the pose in the mol2 file argument to prepare_amber.pl. So in principle one could merely count the number of rescored ligands to determine where to trim the ligand_atom_file input; however, this requires careful attention to detail. In the next release we shall improve the AMBER_SCORE_ID handling. Scott