AMBER Archive (2009)

Subject: [AMBER] Radius for Bromine in MMPBSA calculation

From: john smith (
Date: Thu May 21 2009 - 00:24:05 CDT

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 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/ line 654

After searching the AMEBR Archives, I could not get the correct solution. So
I looked into the 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

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

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