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 <[email protected]> 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 <[email protected]> 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, <[email protected]> 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 [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > Jack > > http://drugdiscoveryathome.com > http://hydrogenathome.org > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > 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 list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
