[gmx-users] Re: Problem with AMBER-GROMACS DNA database residue

Alan alanwilter at gmail.com
Wed Jul 1 11:37:44 CEST 2009

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.


On Wed, Jul 1, 2009 at 10:25, <gmx-users-request at 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.

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