On Wed, Feb 29, 2012 at 8:04 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Feb 28, 2012, Andy Ballard wrote:
> >
> > I am interested in simulating a small organic solute, solvated in water.
> I
> > have a copy of the .prmtop and .coord files for the solute alone (with
> GAFF
> > force field), and from this I would like generate the .prmtop and .coord
> > files for the entire (solute + solvent) system.
>
> > I know that tleap has a solvateBox function which can prepare output
> > topology and coordinate files starting from the solute .pdb file.
> However,
> > since the solute topology file in my possession contains parameters that
> I
> > do not wish to alter, I cannot simply run tleap from scratch (starting
> just
> > from the solute .pdb file), since it could in principle assign the solute
> > force field parameters that differ from my own.
>
> Antechamber has a "top2ff" program that will take your prmtop file and
> create
>
A possible alternative to "top2ff" is extractFrcmod.py -- is that program
in your $AMBERHOME/bin? I can't remember if it was released with
AmberTools 1.5 or not. If so, extractFrcmod.py will dump a force field
file with _every_ parameter in your prmtop file (including all of your VDW
parameters), something I don't think top2ff does. ante-MMPBSA.py will also
dump a full frcmod and full OFF file with every parameter and residue in
your system if you want to use that. You can then load this back into
tleap (after sourcing any other force fields) to override any previous
force field definitions.
If it's not present, you'll have to use top2ff, although there will be more
options in the upcoming AmberTools release.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Feb 29 2012 - 14:30:02 PST
