Hi, Alan Thank you very much for your quick answer. You understand well my problem... I normally use amb2gmx for proteins, and, changing some residue names (ex. CYM-->CYS..), it works correctly... It's the first time that I work with DNA, and I have this problem... thank you for your help Rubben
2009/7/1 Alan <alanwil...@gmail.com> > Hi there, > > Not really clear what you did or want to do, so I'll do assumptions. > > If your have you prmtop and inpcrd files working fine with AMBER (sand > or pmemd) then you just want to run this with GMX (mdrun ...). > > So, you can try amb2gmx.pl program or (better), look at > acpypi.googlecode.com, and you can find how to use 'acpypi' for > converting amber topology files to gromacs topol files. > > Cheers, > Alan > > On Wed, Jul 1, 2009 at 10:25, <gmx-users-requ...@gromacs.org> wrote: > > > > Hi, gmx-users, I have a problem to "translate" nitrogen base residue > names > > from AMBER to GROMACS. > > I have simulated with AMBER a DNA-protein complex, then i have changed in > > the prmtop file the standard nitrogen bases as DT--> DTHY, DG-->DGUA, > > DC-->DCYT, DA-->DADE, in order to "translate" the MDs from AMBER to > > GROMACS... but in the prmtop file are present also DT5, CT3, that > indicate > > the residues at the end of the chains... anyone knows which is the > correct > > GROMACS residue name for these residues? I have searched in the ff.rtp > file > > but seem that these particular residues are not present... > > Thank you in advance... > > > -- > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate > Department of Biochemistry, University of Cambridge. > 80 Tennis Court Road, Cambridge CB2 1GA, UK. > >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><< > _______________________________________________ > gmx-users mailing list 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. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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