http://ambermd.org/formats.html
On Wed, Jan 26, 2011 at 10:31 AM, Baptiste Legrand <bap.legrand.gmail.com>wrote:
> Thanks David. Is a there a new URL to check the format? this one
> http://amber.scripps.edu/formats.html#parm.dat seems down.
> Baptiste
>
> 2011/1/26 case <case.biomaps.rutgers.edu>
>
> > On Wed, Jan 26, 2011, Baptiste Legrand wrote:
> > >
> > > Where can I find the residue topology files? I have a molecule with a
> > > guanidinium which don't seem to be well parametrize with antechamber.
> It
> > > could be helpful to have a look on the ARG guanidinium parameters.
> > Thanks.
> >
> > Look in $AMBERHOME/dat/leap/{parm,prep}. You can find out what atom
> types
> > Amber uses from the all_amino94.in file, and get the parameters
> > corresponding
> > to those atom types from the parm99.dat file.
> >
> > ...good luck....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 26 2011 - 08:00:06 PST
