Re: [AMBER] MMPBSA question

From: Jason Swails <>
Date: Sat, 19 Mar 2011 19:11:16 -0700

On Sat, Mar 19, 2011 at 5:57 PM, Eliac Brown <> wrote:

> If you don't mind, if there is a default value for the non-defined atoms,
> so why sometimes it complains and gives me "bad atom type" error?

It does this if gbsa=2.

> One more question, sorry, is there any option to calculate molecular volume
> f the studied ligand. I spent all the last couple of days trying to find a
> way but I failed.

You definitely *can*. Whether it's implemented in existing AmberTools
software (or other software), I don't know. I've never had any need to
calculate it. If others know something I don't they may chime in.

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Sat Mar 19 2011 - 19:30:02 PDT
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