AMBER Archive (2009)

Subject: Re: [AMBER] Dummy atoms and MM-PBSA

From: Ray Luo (ray.luo_at_uci.edu)
Date: Fri Sep 04 2009 - 13:25:33 CDT

Alireza,

You have to remove LP before MMPBSA analysis.

Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

Alireza Shaneh wrote:
> Hello All,
>
> I want to calculate the binding free energy of my complex, consisting of a MG2+
> ion. Rather than spheric ion, I've defined the geometrical representation of
> the ion in which the octahedral nodes are dummy atoms with zero radii (cationic
> dummy set). Using MM-PBSA, I tried to calculate the binding free energy, but I
> got the following message from the mm-pbsa script:
>
> =>> Calculating energy / entropy contributions
> Calc contrib for ./output/output_com.crd.1
> Calc MM/GB/SAS
> Generate PDB
> Center PDB
> Calc PBSA
> Generate PQR
> No radius found for LP 5797 in residue MD6 314
>
>
> LP is the lone pair atom with no radius. I was hoping if anybody in the
> community has an experience knowing this problem and offers a suggestion.
>
> Thanks,
>
> Alireza
>
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