Re: [gmx-users] Martini Coarse Graining Segmentation Fault using g_fg2cg
Hi, It is better you plan this question in MARtini forum, there are experts that can answer this question! Please register in: http://md.chem.rug.nl/cgmartini/index.php/user-platform/login Rasoul On Thu, Jan 28, 2010 at 1:43 PM, Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de wrote: Dear Gromacs Users, I have performed the Martini Coarse Graining procedure for the simulation of two protein domains by using the two scripts atom2cg.awk and seq2itp.pl. Then I was able to perform my simulation of my coarse grained system. My problem is now to convert my final cg structure into an all atom structure. For this purpose I tried to use the tool g_fg2cg with the inputs containing my fine grained topology ,the coarse grained topology and my coarse grained structure file. But obviously all attempts to apply that tool ended up in a segmentation fault message. I also tried to convert my all atom structure into a cg structure which ended up with the same segmentation fault message. Could you give me some advice on that problem? Here is my screen output: Option Filename Type Description -pfg LOV1_LOV2.pdb.top InputTopology file -pcg martini_v2.0_example.top Input, Opt! Topology file -c lov1lov2_42ns_27.1.pdb InputGeneric trajectory: xtc trr trj gro g96 pdb -oout.gro Output Generic structure: gro g96 pdb xml Option Type Value Description -- -[no]h bool no Print help info and quit -niceint 0 Set the nicelevel -nint 0 1: fg2cg transformation, 0: cg2fg transformation -watint 0 1: rewrites FG_CG water to true fg water; -rad real0.3 A radius for random atom insertion; calling cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 NOTE: System has non-zero total charge: -2.98e+00 # G96BONDS: 2738 # G96ANGLES: 3994 # PDIHS: 1465 # IDIHS: 1328 # LJ14: 4520 calling cpp... processing topology... Generated 0 of the 465 non-bonded parameter combinations Excluding 1 bonded neighbours for Protein 1 Excluding 1 bonded neighbours for ProteinB 1 NOTE: System has non-zero total charge: -6.00e+00 Number of fg atoms 2696 Number of cg atoms 571 Reading frame 0 time 42000.004 1264673691 Segmentation fault When I applied this tool on the ubiquitin example I had another problem, but I did it in the same way as before. Here is the screen output: Option Filename Type Description -pfg 1ubq.top InputTopology file -pcg out3.top Input, Opt! Topology file -c 1UBQ.gro InputGeneric trajectory: xtc trr trj gro g96 pdb -oout.gro Output Generic structure: gro g96 pdb xml Option Type Value Description -- -[no]h bool no Print help info and quit -niceint 0 Set the nicelevel -nint 1 1: fg2cg transformation, 0: cg2fg transformation -watint 0 1: rewrites FG_CG water to true fg water; -rad real0.3 A radius for random atom insertion; calling cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 2 bonded neighbours for SOL 58 # G96BONDS: 766 # G96ANGLES: 1107 # PDIHS: 428 # IDIHS: 334 # LJ14: 1304 # SETTLE: 58 calling cpp... cpp: out3.top: Datei oder Verzeichnis nicht gefunden cpp: warning: '-x c' after last input file has no effect cpp: no input files cpp exit code: 256 Tried to execute: 'cpp -I/pc50417/pee18323/REVERSE_trans_gromacs/agromacs-reverse/share/top out3.top grompp605Sk3' The 'cpp' command is defined in the .mdp file processing topology... Number of fg atoms 934 Number of cg atoms 0 Reading frames from gro file 'UBIQUITIN', 934 atoms. Reading frame 0 time0.000 out.xtc Last frame 0 time0.000 Back Off! I just backed up out.gro to ./#out.gro.2# Cg structure computed ! In that case out.gro did not contain any atoms. Thanks for any suggestions! Best regards, Emanuel Peter -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list
[gmx-users] Re: including a custom itp file in topology
Hi Jack, Look, if I understand well, what you want is to be able to something like tleap does for amber, where you load all the libs you need, including the ones you created for your ligand(s), and then generate the MD input files at once needing just the complexed pdb or mol2 as input. For pdb2gmx to do the same, you would need to tweak the files /gromacs/top/ffamber99sb.rtp, hdb etc., which I once considered doing that for acpypi but then it would add much more complexity for no much gain. What I hope is for the new *pdb2gmx* (gmx 4.1 maybe? or only for gmx 5.0?) to feature, among other things, this capability as you requested. Cheers, Alan On Thu, Jan 28, 2010 at 17:13, Jack Shultz j...@drugdiscoveryathome.comwrote: Hi, I was trying to figure out if there is a short-cut for what I'm doing. I have complexes that I'm trying to prep using pdb2gmx. The ligand does not have a standard residue name. The way I know this can work is seperating out the ligand and protein into seperate files and preping the ligand using acpypi and the protein using pdb2gmx. Then incorporating them into a single pdb complex and including a reference to the ligand.itp (generated by acpypi) into a complex topology file. Is there any shortcut to doing this? any way to reference the ligand's itp file when running pdb2gmx? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Re: including a custom itp file in topology
Hi, I don't understand exactly what is the requested feature here. I am currently reorganizing the force field setup in Gromacs to more cleanly support AMBER and CHARMM and adding some extra functionality. I started a discussion on the gmx-developers list on this topic. On feature I have added is that rtp, hdb, etc files no longer have fixed names and you can have multiple of them. So you can just put, e.g., a file called ligand.itp in your force field or current dir and pdb2gmx will read it. Berk From: alanwil...@gmail.com Date: Fri, 29 Jan 2010 09:20:31 + To: j...@drugdiscoveryathome.com CC: gmx-users@gromacs.org; a...@drugdiscoveryathome.com Subject: [gmx-users] Re: including a custom itp file in topology Hi Jack, Look, if I understand well, what you want is to be able to something like tleap does for amber, where you load all the libs you need, including the ones you created for your ligand(s), and then generate the MD input files at once needing just the complexed pdb or mol2 as input. For pdb2gmx to do the same, you would need to tweak the files /gromacs/top/ffamber99sb.rtp, hdb etc., which I once considered doing that for acpypi but then it would add much more complexity for no much gain. What I hope is for the new *pdb2gmx* (gmx 4.1 maybe? or only for gmx 5.0?) to feature, among other things, this capability as you requested. Cheers,Alan On Thu, Jan 28, 2010 at 17:13, Jack Shultz j...@drugdiscoveryathome.com wrote: Hi, I was trying to figure out if there is a short-cut for what I'm doing. I have complexes that I'm trying to prep using pdb2gmx. The ligand does not have a standard residue name. The way I know this can work is seperating out the ligand and protein into seperate files and preping the ligand using acpypi and the protein using pdb2gmx. Then incorporating them into a single pdb complex and including a reference to the ligand.itp (generated by acpypi) into a complex topology file. Is there any shortcut to doing this? any way to reference the ligand's itp file when running pdb2gmx? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: including a custom itp file in topology
Hi Berk, If pdb2gmx will do what you said below, then for me the feature is delivered. To be sure, what I would like to have (and I guess Jack too) is: - one has a pdb with protetin + ligands (one or more) - have the topologies itp files for the ligands already created - run pdb2gmx on complex.pdb and have pdb2gmx to *know* about the ligands and generated the respective top and gro files ready for EM and MD. It is that what I understood Jack wants and what you said you have added to the coming pdb2gmx (for gmx 4.1?). Many thanks, Alan On Fri, Jan 29, 2010 at 09:28, gmx-users-requ...@gromacs.org wrote: From: Berk Hess g...@hotmail.com Hi, I don't understand exactly what is the requested feature here. I am currently reorganizing the force field setup in Gromacs to more cleanly support AMBER and CHARMM and adding some extra functionality. I started a discussion on the gmx-developers list on this topic. On feature I have added is that rtp, hdb, etc files no longer have fixed names and you can have multiple of them. So you can just put, e.g., a file called ligand.itp in your force field or current dir and pdb2gmx will read it. Berk -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Structure deformation
Hi everyone, I have a question about structure deformation Can pdb2gmx alter secondary structures of my protein, while adding hydrogens. Because I had a helix in my protein, that became a beta-sheet after pdb2gmx. What may be the problem? Thank you Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: including a custom itp file in topology
Dear Berk, I beg your pardon, but I have to assume that what you wrote below is not correct so, right? Should it be 'ligand.rtp' instead of 'ligand.itp'? Once I have my hands on this new pdb2gmx, I believe I can tweak acpypi to generate rtp files as well (but hdb and else probably not). Cheers, Alan On Fri, Jan 29, 2010 at 11:00, gmx-users-requ...@gromacs.org wrote: of them. So you can just put, e.g., a file called ligand.itp in your force field or current dir and pdb2gmx will read it. -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Structure deformation
Carla Jamous wrote: Hi everyone, I have a question about structure deformation Can pdb2gmx alter secondary structures of my protein, while adding hydrogens. Because I had a helix in my protein, that became a beta-sheet after pdb2gmx. Sorry to say, but this sounds completely unlikely. A bug of this magnitude surely would've been noticed long ago. What may be the problem? Are you certain you're looking at the same residues? pdb2gmx renumbers from 1, so if there are missing N-terminal residues, they will not have the same numbers before and after pdb2gmx. -Justin Thank you Carla -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: including a custom itp file in topology
I confess I don't know the difference between rtp and itp. What I was hoping was an easier way to generate topologies for complexes that have non-standard residue names like LIG. Alan's acpypi works. You just have to do some extra scripting. But it seems like pdb2gmx should have a way to load the files describing the non-standard residue names directly. On Fri, Jan 29, 2010 at 6:24 AM, Alan alanwil...@gmail.com wrote: Dear Berk, I beg your pardon, but I have to assume that what you wrote below is not correct so, right? Should it be 'ligand.rtp' instead of 'ligand.itp'? Once I have my hands on this new pdb2gmx, I believe I can tweak acpypi to generate rtp files as well (but hdb and else probably not). Cheers, Alan On Fri, Jan 29, 2010 at 11:00, gmx-users-requ...@gromacs.org wrote: of them. So you can just put, e.g., a file called ligand.itp in your force field or current dir and pdb2gmx will read it. -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: xmgrace
Hi all, I have recently started working with GROMACS , and I am not able to find xmgrace in GROMACS folder . Do I have to download the file separately ?? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: xmgrace
Hi all, I have recently started working with GROMACS , and I am not able to find xmgrace in GROMACS folder . Do I have to download the file separately ?? -- Bharat M.Sc. Bioinformatics (Final year) Centre for Bioinformatics Pondicherry University Puducherry India Mob. +919962670525 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: xmgrace
bharat gupta wrote: Hi all, I have recently started working with GROMACS , and I am not able to find xmgrace in GROMACS folder . Do I have to download the file separately ?? Yes, it is a separate program. Search Google. -Justin Thanks -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Structure deformation
Carla Jamous wrote: Thank you Justin, you were right I was looking at the wrong residue numbers. I have another question that may also sound stupid, but I can't figure it out: I want to extract from my trajectory, the protein, the ligand and ions. However, when I try to do that with trjconv -f .trr -s .trr -n .ndx gromacs asks to choose a group from my index file. But if I choose group 0 1 2 it only takes the first group without the rest. So how can I extract many groups at once from my trajectory? Use make_ndx to merge the desired groups (i.e., 0 | 1 | 2) or simply !12 (assuming group 12 is SOL). -Justin Carla On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, I have a question about structure deformation Can pdb2gmx alter secondary structures of my protein, while adding hydrogens. Because I had a helix in my protein, that became a beta-sheet after pdb2gmx. Sorry to say, but this sounds completely unlikely. A bug of this magnitude surely would've been noticed long ago. What may be the problem? Are you certain you're looking at the same residues? pdb2gmx renumbers from 1, so if there are missing N-terminal residues, they will not have the same numbers before and after pdb2gmx. -Justin Thank you Carla -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Structure deformation
Thank you Justin, you were right I was looking at the wrong residue numbers. I have another question that may also sound stupid, but I can't figure it out: I want to extract from my trajectory, the protein, the ligand and ions. However, when I try to do that with trjconv -f .trr -s .trr -n .ndx gromacs asks to choose a group from my index file. But if I choose group 0 1 2 it only takes the first group without the rest. So how can I extract many groups at once from my trajectory? Carla On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, I have a question about structure deformation Can pdb2gmx alter secondary structures of my protein, while adding hydrogens. Because I had a helix in my protein, that became a beta-sheet after pdb2gmx. Sorry to say, but this sounds completely unlikely. A bug of this magnitude surely would've been noticed long ago. What may be the problem? Are you certain you're looking at the same residues? pdb2gmx renumbers from 1, so if there are missing N-terminal residues, they will not have the same numbers before and after pdb2gmx. -Justin Thank you Carla -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: including a custom itp file in topology
Hi, rtp stands for 'Residue ToPology' and is used exclusively for building block definitions, which are only used by pdb2gmx. itp stands for 'Include ToPology' and can contain any part of a topological description of a system, atom types, bond types, moleculetypes, definitions, to be #included at the right point in the master topology file. It is often used to separate out moleculetype definitions, but also the top level force field parameters are contained in a .itp file (ffoplsaa.itp for example). For non standard residues, the residue has to be defined as a building block and put in to a .rtp file in order to allow pdb2gmx to process it. Non-bonded ligands need not be processed by pdb2gmx. With a proper description in terms of coordinates and [ moleculetype ] (.itp file), they can be easily merged with coordinates, c.q. topology as produced by pdb2gmx. Hope it helps, Tsjerk On Fri, Jan 29, 2010 at 1:45 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: I confess I don't know the difference between rtp and itp. What I was hoping was an easier way to generate topologies for complexes that have non-standard residue names like LIG. Alan's acpypi works. You just have to do some extra scripting. But it seems like pdb2gmx should have a way to load the files describing the non-standard residue names directly. On Fri, Jan 29, 2010 at 6:24 AM, Alan alanwil...@gmail.com wrote: Dear Berk, I beg your pardon, but I have to assume that what you wrote below is not correct so, right? Should it be 'ligand.rtp' instead of 'ligand.itp'? Once I have my hands on this new pdb2gmx, I believe I can tweak acpypi to generate rtp files as well (but hdb and else probably not). Cheers, Alan On Fri, Jan 29, 2010 at 11:00, gmx-users-requ...@gromacs.org wrote: of them. So you can just put, e.g., a file called ligand.itp in your force field or current dir and pdb2gmx will read it. -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: xmgrace
Thanks sir But there is one problem that when I am running the mdrun step of 5th step of lysozyme tutorial, I am getting an error :- Can not open file: topol.tpr Can u tell me how to rectify it .. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: xmgrace
bharat gupta wrote: Thanks sir But there is one problem that when I am running the mdrun step of 5th step of lysozyme tutorial, I am getting an error :- Can not open file: topol.tpr Can u tell me how to rectify it .. No, since you haven't provided the command line you're using or what the tutorial is expecting you to do. If this is unrelated to your original post, please start a new thread so the archive doesn't get confusing. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Plot renumbering
Hello friends, As Justin replied at carla query about structure deformation after the pdb2gmx the new number retain till end. My PDB starts at 24 to 200 aa, While running xmgrace (after complete simulation) the rmsd plot is from 1 to 176aa. I understood by previous mail that gromacs renumbered my pdb file at first step. My question is, Is their any way to get plot from 24 to 200 (as entry in pdb) rather 1 to 174 ? Regard Rituraj On Fri, Jan 29, 2010 at 7:28 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Structure deformation (Carla Jamous) 2. Re: Structure deformation (Justin A. Lemkul) 3. Re: Re: including a custom itp file in topology (Tsjerk Wassenaar) 4. Re: RE: xmgrace (bharat gupta) 5. Re: RE: xmgrace (Justin A. Lemkul) 6. Re: RE: xmgrace (Baofu Qiao) -- Message: 1 Date: Fri, 29 Jan 2010 14:03:12 +0100 From: Carla Jamous carlajam...@gmail.com Subject: Re: [gmx-users] Structure deformation To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: e02c90f11001290503yce52eb7w45f7f23a53250...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Thank you Justin, you were right I was looking at the wrong residue numbers. I have another question that may also sound stupid, but I can't figure it out: I want to extract from my trajectory, the protein, the ligand and ions. However, when I try to do that with trjconv -f .trr -s .trr -n .ndx gromacs asks to choose a group from my index file. But if I choose group 0 1 2 it only takes the first group without the rest. So how can I extract many groups at once from my trajectory? Carla On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, I have a question about structure deformation Can pdb2gmx alter secondary structures of my protein, while adding hydrogens. Because I had a helix in my protein, that became a beta-sheet after pdb2gmx. Sorry to say, but this sounds completely unlikely. A bug of this magnitude surely would've been noticed long ago. What may be the problem? Are you certain you're looking at the same residues? pdb2gmx renumbers from 1, so if there are missing N-terminal residues, they will not have the same numbers before and after pdb2gmx. -Justin Thank you Carla -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100129/55ff7a64/attachment-0001.html -- Message: 2 Date: Fri, 29 Jan 2010 08:04:11 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Structure deformation To: Gromacs Users' List gmx-users@gromacs.org Message-ID: 4b62dccb.8030...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Carla Jamous wrote: Thank you Justin, you were right I was looking at the wrong residue numbers. I have another question that may also sound stupid, but I can't figure it out: I want to extract from my trajectory, the protein, the ligand and ions. However, when I try to do that with trjconv -f .trr -s .trr -n .ndx gromacs asks to choose a group from my index file. But if I choose group 0 1 2 it only takes the first group without the rest. So how can I extract many groups at once from my trajectory? Use make_ndx to merge the desired groups (i.e., 0 | 1 | 2) or simply !12 (assuming group 12 is SOL). -Justin Carla On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone
Re: [gmx-users] Plot renumbering
rituraj purohit wrote: Hello friends, As Justin replied at carla query about structure deformation after the pdb2gmx the new number retain till end. My PDB starts at 24 to 200 aa, While running xmgrace (after complete simulation) the rmsd plot is from 1 to 176aa. I understood by previous mail that gromacs renumbered my pdb file at first step. My question is, Is their any way to get plot from 24 to 200 (as entry in pdb) rather 1 to 174 ? Write a script that renumbers the file - perl, awk, sed, etc. I think pdb2gmx renumbering is being removed in the development code for future versions, FYI. -Justin Regard Rituraj On Fri, Jan 29, 2010 at 7:28 PM, gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org mailto:gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org mailto:gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Structure deformation (Carla Jamous) 2. Re: Structure deformation (Justin A. Lemkul) 3. Re: Re: including a custom itp file in topology (Tsjerk Wassenaar) 4. Re: RE: xmgrace (bharat gupta) 5. Re: RE: xmgrace (Justin A. Lemkul) 6. Re: RE: xmgrace (Baofu Qiao) -- Message: 1 Date: Fri, 29 Jan 2010 14:03:12 +0100 From: Carla Jamous carlajam...@gmail.com mailto:carlajam...@gmail.com Subject: Re: [gmx-users] Structure deformation To: jalem...@vt.edu mailto:jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: e02c90f11001290503yce52eb7w45f7f23a53250...@mail.gmail.com mailto:e02c90f11001290503yce52eb7w45f7f23a53250...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Thank you Justin, you were right I was looking at the wrong residue numbers. I have another question that may also sound stupid, but I can't figure it out: I want to extract from my trajectory, the protein, the ligand and ions. However, when I try to do that with trjconv -f .trr -s .trr -n .ndx gromacs asks to choose a group from my index file. But if I choose group 0 1 2 it only takes the first group without the rest. So how can I extract many groups at once from my trajectory? Carla On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, I have a question about structure deformation Can pdb2gmx alter secondary structures of my protein, while adding hydrogens. Because I had a helix in my protein, that became a beta-sheet after pdb2gmx. Sorry to say, but this sounds completely unlikely. A bug of this magnitude surely would've been noticed long ago. What may be the problem? Are you certain you're looking at the same residues? pdb2gmx renumbers from 1, so if there are missing N-terminal residues, they will not have the same numbers before and after pdb2gmx. -Justin Thank you Carla -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100129/55ff7a64/attachment-0001.html -- Message: 2 Date: Fri, 29 Jan 2010 08:04:11 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Re: [gmx-users] opla atom types and charges for nitrile / thienopyridine
Sebastian Kruggel wrote: hello, i generated a lig.itp file with topolgen.pl to perform ligand/protein md simulations. as my ligand contains nitriles and a thienopyridine scaffold, topolgen failed assigning atom types. i found opls_753/4 in ffoplsaa.atp for the nitrile but changing the *itp file i didn't find any hint for the charge nor the chgr entry to put. See below for parameterization advice. See the manual for information on charge groups - the .atp file won't help you there. additionally i am not sure about the treatment of the pyridine nitrogen as i only see the opls_520 and i don't know what the 6-31G* is meaning. 6-31G* is a QM charge calculation method often used in deriving parameters; see below. in the mailing list i found http://lists.gromacs.org/pipermail/gmx-users/2009-May/042069.html The more applicable message in the thread above is actually the next message: http://lists.gromacs.org/pipermail/gmx-users/2009-May/042068.html Virtual sites can be tricky with the nitrile group. but wondered if oplsaa shouldn't be the better choice for a md simulation of ligand and protein - or is the gromos53a6 (or the gmx force field as used in the drug/enzyme tutorial http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf ) not too bad? Either way, parameterization is going to be hard. Please consult the following, and consider that deriving parameters for any new species is a very advanced topic and should only be undertaken with a thorough knowledge of derivation procedures and the intrinsics of the desired force field: http://www.gromacs.org/Documentation/How-tos/Parameterization You could certainly derive parameters suitable for either force field (OPLS or 53a6), but it will take a considerable amount of time. The topolgen.pl script is just a cute little utility I wrote some time ago to give you a starting point for topology generation. Its output should not necessarily be considered accurate or appropriate for immediate simulation, anyway. You've got to do the legwork of deriving parameters from there! -Justin maybe anybody has done simulations with similar molecules, thanks in advance for any help! sebastian -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with gromacs-openMM
Thanks a lot!!! it works Hi, try to do add the OpenMM library dir to your library path before running make $ export LD_LIBRARY_PATH=/opt/openmm/lib:$LD_LIBRARY_PATH Also, OpenMM support will be officially available in the next Gromacs release (soon). Rossen On 1/27/10 4:28 AM, jorge_quint...@ciencias.uis.edu.co wrote: make[3]: *** No hay ninguna regla para construir el objetivo `/usr/local/openmm/lib/libOpenMM.*', necesario para `grompp'. Alto. make[3]: se sale del directorio `/root/gromacs-4.0.7/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: se sale del directorio `/root/gromacs-4.0.7/src' make[1]: *** [all] Error 2 make[1]: se sale del directorio `/root/gromacs-4.0.7/src' make: *** [all-recursive] Error 1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: opls atom types and charges
hi justin, thanks for the quick answer and ... Either way, parameterization is going to be hard. so you don't think the use of default parameters of gmx-ff as described in the drug-enzyme-tutorial to be useful (to give reasonable results) if i want to get an impression of the stability of docked poses and for the calculation of binding free energies? simulations don't crash the way described in http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf - i only thought that oplsaa would probably be the 'better choice'? thanks for your estimation, sebastian -- Sebastian Kruggel Institut für Pharmazie Bundesstr. 45 | Raum 112 (406) D 20146 Hamburg Tel: +49 (0)40 42838-3626 (-3484) mail: krug...@chemie.uni-hamburg.de http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Dihedral time of circulation
Dear Sa?a: There are many dihedral angles in the MET sidechain. I suspect that you mean to ask how long does it take the chi1 dihedral angle of MET to equilibrate rotametric preference? The answer is entirely dependent on context, with a free amino acid (perhaps also a methionine dipeptide) having the lowest correlation time. This time, however, will always be very long on simulation timescales. Note also that the time required in simulation may or may not match an experimental value if one exists. If you want to get a lower bound for the time required, I suggest that you put a methionine dipeptide (or free methionine if you must) in vacuum and use the sd integrator. You should be able to get hundreds of us per day on a system like this. Obviously the time that you observe here will be significantly less than the time required in bulk water, and the time required in a solvated protein context is likely larger, and in the context of a protein embedded in a lipid bilayer this will be even larger. Still, this is a simple method to find out some number that represents the absolute fastest that this could occur. I do realize that the sd integrator time does not map directly to that of the md integrator for kinetics (with a given tau_t), but this isn't intended to be all that accurate, just to be something that you could probably calculate in one day. If you need something more accurate then it will take you longer. (You could use the md integrator in a box of water with PME for example, but that will be much more expensive -- putting a few METs in the same box might be useful here if you position restrain a single backbone atom to ensure that they do not contact each other). Chris. -- original message -- I have a question about dihedral time of circulation: what is the typical time for a rotation of 360 deg of an unconstrained dihedral in the side chain of an amino acid at 300K ? For example dihedral rotation of MET side chain in a ALA-MET-ALA side chain. A use OPLSAA/tip4p FF. Many thanks Sa?a -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Lambda and simulation problem
Hello everybody, I performed 100 simulation using a lambda step of 0.01 using gromacs 4.0.5 and Amber forcefield, starting always from the same structure ( a crystal with the ligand), minimizing for 3000 step and then starting the md simulation. Here the row about the changing atom in my .itp file 15 amber99_48 1 M5P S151 -0.716232.0600 amber99_43 -0.729416. and this is the mdp file concerning the free energy calculation: free_energy = yes sc_power= 1.0 sc_alpha= 0.5 sc_sigma= 0.3 delta_lambda= 0.0 init_lambda = 0.50 I succesfully wrote the topology for the alchemical transformation and in both end simulations ( with Lambda =0 and Lambda =1) I have no problem. For the intermediate steps( i.e. lambda=0.5) , however, I found that the Jennard-Jones and the Coulomb interactions are drammatically wrong. Actually, the S-O atom seems desappeared and the aminoacids in the active site change their position in order to reach a good equilibrium as if the S-O was not there ( there are charded atoms all around). Moreover the changing atom moves around going crushing against the other atoms sorrounding without apparent problems. How could it be? Can someone help me? Thank you! -- Ph.D. Student Matteo De Chiara Dept. of Molecular Biology, University of Siena Via Fiorentina 1, 53100 Siena Italy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: opls atom types and charges
Sebastian Kruggel wrote: hi justin, thanks for the quick answer and ... Either way, parameterization is going to be hard. so you don't think the use of default parameters of gmx-ff as described in the drug-enzyme-tutorial to be useful (to give reasonable results) if i want to get an impression of the stability of docked poses and for the calculation of binding free energies? simulations don't crash the way described in http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf - i only thought that oplsaa would probably be the 'better choice'? From experience I can tell you that PRODRG parameters, at face value, are generally unreliable. The charges and charge groups it provides do not give good results when put through the tests that proper parameters should. This is not always the case (depending on the complexity of your molecule), but for the compounds I have dealt with, this has definitely been true. PRODRG is a nice tool because it saves you the work of building a topology from scratch, but it is still your job to come up with parameters consistent with the original derivation of the force field. As for the better choice, all force fields have pros and cons. It's your job to read the literature for what's known about each and make an intelligent choice. This is not a trivial decision, and can heavily influence the results you get. Using the ffgmx force field (as in the tutorial) is an especially bad idea, since (as pdb2gmx warns you) this force field is ancient and deprecated. -Justin thanks for your estimation, sebastian -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:Dihedral time of circulation
Dear all, perhaps I have to be more clear: I made I short MD with OPLSAA/tip4p and PME of Gly-Met-Gly. If I plot the CB-CG-SD-CE dihedral on the time scale I get the shortest time for a whole rotation of about 100 fs. So, my question is, if this value is reasonable or not? I suppose there must be some experimental data or should I expect this time scale. Sasa -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ Saa Bjelic, PhD Structural Biology and Biophysics Life Science, OFLC 105 Paul-Scherrer-Institute CH-5232 Villigen PSI Switzerland Phone: +41-(0)56 310 5295 Fax:+41 56 310 5288 -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Dihedral time of circulation
100 fs = 50 timesteps? I doubt it, but then again I have never checked and you're talking about a chi3 here, and one that involves a S with no hydrogens at that so I guess that it could occur quicker than I expected. However, you should avoid talking about time for one rotation without error bounds here as it's also possible that you are seeing some non-equilibrium equilibration to relieve bad contacts in your initial structure. -- original message -- Dear all, perhaps I have to be more clear: I made I short MD with OPLSAA/tip4p and PME of Gly-Met-Gly. If I plot the CB-CG-SD-CE dihedral on the time scale I get the shortest time for a whole rotation of about 100 fs. So, my question is, if this value is reasonable or not? I suppose there must be some experimental data or should I expect this time scale. Sasa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
