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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Received on Thu May 21 2009 - 08:35:09 PDT
