John,
The error messages in your log files are not related to the pb or gb
calculation by sander, but related to the sa calculation by molsurf. If you
do a search of your error message in the mailing list archive, you should be
able to find the solution for it.
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.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of john smith
Sent: Sunday, May 24, 2009 9:53 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Radius for Bromine in MMPBSA calculation
Dr. Luo
I have attached the mmpbsa input files and the log files for the two
ligands for which i am not able to complete the calculation due to
error in bromine radius.
The error which i recievedat the terminal is as follows
1. For m12 ligand
Died at /opt/amber10/src/mm_pbsa/mm_pbsa_calceneent.pm line 652, <PDB>
line 5657.
2. For m13 ligand
Died at /opt/amber10/src/mm_pbsa/mm_pbsa_calceneent.pm line 652, <PDB>
line 5659.
What can be the possible solution to this problem?
Regards
-John
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Received on Tue May 26 2009 - 01:13:07 PDT
