Re: [AMBER-Developers] Testing Periodic ICCG pbsa solver under MMPBSA

From: Jason Swails <>
Date: Thu, 14 Feb 2013 21:45:09 -0500

I don't know how easy it will be to set up to work with periodic
boundary conditions, since it always strips the box information and solvent.

If it doesn't require box info in the trajectory/topology file, you can use
-make-mdins to generate the mdin files, modify those variables as needed
(_MMPBSA_pb.mdin), and then re-run using -use-mdins. If everything works,
then we can add those variables to the input file pretty easily.
 If needs substantial changes it may have to wait...

Hope this helps,

On Thu, Feb 14, 2013 at 7:01 PM, <> wrote:

> Hello everyone,
> I am working on a modifying the ICCG solver for pbsa to work for
> periodic boundary conditions. I am at the stage of testing it for use
> under the MMPBSA to confirm it provides proper results for binding
> energy calculations.
> Currently it is bound to solvopt=8 with bcopt=10. Unfortunately, when I
> put these options into the &pb namelist of my file, MMPBSA
> returns an error of:
> "Unknown variable bcopt in &pb"
> I have tracked the message to a line in the "" file for
> MMPBSA, but I am not sure what needs to be done from here.
> -Wesley Botello-Smith
> _______________________________________________
> AMBER-Developers mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Thu Feb 14 2013 - 19:00:02 PST
Custom Search