AMBER Archive (2002)

Subject: mm_pbsa output error

From: Michael Murray (mimurra3_at_vt.edu)
Date: Mon Sep 23 2002 - 12:26:11 CDT

All,

We seem to be having trouble running mm_pbsa in Amber7. The simulation
proceeds as expected creating output files for the ligand, receptor,
and complex. However, an error message is output before the
statistics.out file is created. The run ends with this error:

Use of uninitialized value in multiplication (*) at
/usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1234.
Use of uninitialized value in multiplication (*) at
/usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1202.
Use of uninitialized value in multiplication (*) at
/usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1202.
Use of uninitialized value in multiplication (*) at
/usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1323.
Use of uninitialized value in multiplication (*) at
/usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1323.
Use of uninitialized value in multiplication (*) at
/usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1323.
Use of uninitialized value in multiplication (*) at
/usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1323.
     No data for 0+0 GB GB 0

I am unsure what to make of this. Upon looking at the *rec.all.out
file as well as the *com.all.out file there seems to be something wrong
with EGB field in several of the steps. For some of the snapshots the
EGB result is 'nan' while in others it produces the expected value.
Could our output errors have something to do with this value? Does
anybody know what this might indicate? The log file says that the
entries for PB must be overwritten but I'm not sure where they come
from. Any information that could be provided will be extremely
helpful. Relevant files can be found at:
http://filebox.vt.edu/users/mimurra3/mm_pbsa/

thank you,

Mike

-------------------------------
Michael Murray
Dept. of Biochemistry
201 Engel Hall
Virginia Polytechnic Institute and State University
Blacksburg, VA 24061-0308