AMBER Archive (2009)

Subject: RE: [AMBER] Radius for Bromine in MMPBSA calculation

From: Ray Luo (ray.luo_at_uci.edu)
Date: Thu May 21 2009 - 11:32:41 CDT

Please provide more information, at least your mmpbsa input script.

All the best,
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/
==========================================

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
Of john smith
Sent: Wednesday, May 20, 2009 10:24 PM
To: AMBER Mailing List
Subject: [AMBER] Radius for Bromine in MMPBSA calculation

Hi All,
I am performing MM/PBSA calculations for studying protein ligand
interactions. One of my ligand contains Bromine attached to an aromatic
ring. I have successfully completed the molecular dynamics simulation and
extracted the snapshots of complex, receptor and the ligand. However when I
run the mm_pbsa.pl script for binding energy calculation, it terminates with
the following error.

No radius for Br1 5655 in residue 12o 353 ( in the log file)

Died at /../src/mm_pbsa/mm_pbsa_calceneent.pm line 654

After searching the AMEBR Archives, I could not get the correct solution. So
I looked into the mm_pbsa_calceneent.pm file and identified the lines (line
562-571 & 578-587) which contains radii for different atoms. I tried adding
van der Waals radius for Bromine as 1.85 below this line, and the script
runs.

So I want to know whether this is the correct procedure for the solving my
problem or any other changes need to be done in the
mm_pbsa_calceneent.pmfile and what is the correct van der Waals radius
for Bromine

Please suggest an appropriate solution
Thanks in advance

-John
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