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
the force field files that correspond to it. Then you can load those into
tleap, and use the solvateBox or solvateOct routines as usual. In that way
your force field parameters won't change.
If you really just got the solute prmtop file from GAFF, you could also just
rerun antechamber to regenerate the library files (.prep or .mol2 format),
then use those again in tleap. LEaP doesn't reassign force fields--it just
copies whatever it finds in the library files to the output prmtop file.
...good luck....dac
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Received on Wed Feb 29 2012 - 05:30:02 PST
