[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] 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] 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
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
