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

Rubben Torella rubben.torella at gmail.com
Wed Jul 1 12:08:21 CEST 2009

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

2009/7/1 Alan <alanwilter at 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-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.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
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