AMBER Archive (2009)

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

From: Ray Luo (ray.luo_at_uci.edu)
Date: Mon May 25 2009 - 16:10:41 CDT


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_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: 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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