Re: [AMBER-Developers] Creating a solvation box for all atom MD from output of a GB calculation

From: Jason Swails <>
Date: Tue, 6 Oct 2015 11:27:36 -0400

On Tue, Oct 6, 2015 at 11:19 AM, Istvan Kolossvary <>

> Hi,
> I have the prmtop and inpcrd file from an LMOD docking calculation in
> AmberTools. The system includes a cofactor and a ligand with gaff
> parameters. How can I transform this system to an explicitly solvated
> system with water molecules and ions in a periodic box for all atom MD
> simulation, preserving the gaff parameters? Ultimately, I'll need a new
> prmtop and inpcrd file. I don't have access to Amber, only AmberTools.

​Presumably to make the prmtop in the first place you needed a mol2 file
defining the cofactor residue and an frcmod file with the missing
parameters from gaff. You will also need a PDB file of your complex (you
can use ambpdb to convert the prmtop/inpcrd combo into a PDB file).

Then you need to load the mol2 file, frcmod parameters, gaff parameters,
and protein force field into tleap, followed by the PDB file. You can then
use solvateBox/solvateOct to add a solvent box around your system. Your
tleap script will look something like this:

source leaprc.gaff
​source leaprc.ff14SB
RES = loadMol2​ cofactor.mol2
loadAmberParams cofactor.frcmod

mol = loadPDB complex.pdb
solvateOct mol 12.0 TIP3PBOX

saveAmberParm mol solvated.prmtop solvated.inpcrd

If you do not already have the frcmod and mol2 files, you can use ParmEd to
create an frcmod and OFF file that you can load with the relevant


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Tue Oct 06 2015 - 08:30:04 PDT
Custom Search