Re: [AMBER] binding energy calculation problem

From: <>
Date: Thu, 17 Feb 2011 10:21:43 -0500 (EST)


> /opt/amber11/bin/sander -O -i -o pbsa_com.1.out -c
> ./snapshot_com.crd.1 -p ./1q3w_out.prmtop not successfu

this is the actual command that failed. You could run it by hand and see
what the output says. pbsa can sometimes crash on unusual, large (or even
random?) conformations, often the output file will contain an explanation
or a suggestion of what parameter to change.

In the worst case, you could do the MMPBSA analysis without data from that
one problematic snapshot.


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Thu Feb 17 2011 - 07:30:05 PST
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