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

From: Istvan Kolossvary <istvan.kolossvary.hu>
Date: Tue, 06 Oct 2015 11:19:06 -0400


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.

Many thanks,


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Received on Tue Oct 06 2015 - 08:30:03 PDT
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