Re: AMBER: pbsa calculation on part of the molecule

From: Ray Luo <>
Date: Wed, 19 May 2004 13:31:50 -0700

Group input has never been tested in pbsa. An issue also unclear in
these types of calculations is how we should treat the environment
outside the selected residues: bulk water or rest of the protein?

If the environment is bulk water, you can just truncate the selected
residues by yourself and regenerate a prmtop file for a separate pbsa
run. If the environment is the rest of the protein, you need to wait for
the next update of pbsa coming out later this year.


S. Frank Yan wrote:

>I was wondering if there's a way to carry out the PBSA calculation on
>part of the molecule, like within 20 angstrom of the active site. This
>most likely results from belly simulation of a partially solvated
>system. I tried to set the group in pbsa input, but the error message
>GRP 1 RES 190 TO 206
> Number of atoms in this group = 2696
> ----- END OF GROUP READ -----
> When igb>0, the moving part must be at the
> start of the molecule. This does not seem
> to be the case here.
> natbel,i,igroup(i) = 2696 2757
> 1
>Thanks a lot,
>The AMBER Mail Reflector
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Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail:
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Received on Thu May 20 2004 - 22:53:00 PDT
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