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<< _______________________________________________ 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
