Hi,
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.
So is there a way to generate the .prmtop and .coord files for the
solute-solvent system from the .prmtop and .coord files for the solute? Or
is there a way to circumvent this problem?
Thanks in advance for any help,
Andy Ballard
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 28 2012 - 08:00:02 PST
