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)
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