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
