AMBER Archive (2009)

Subject: RE: [AMBER] MM-PBSA nmode statistics

From: Ray Luo (ray.luo_at_uci.edu)
Date: Mon Jun 01 2009 - 14:05:48 CDT

Dimitry,

If you look at the raw data for the snapshots as listed in
"ras_raf_II_wt_lig.all.out" and "ras_raf_II_wt_statistics.out.snap". Your
data are already different from those in the saved files. The difference in
the raw data causes the discrepancy, not the perl script.

If you can make sure your nmode binary is okay, then the discrepancy in the
test probably comes from the different inpcrd files from those that Dr.
Gohlke used to generate the saved files. We observed the same discrepancy
when we tested this example. I think it is okay.

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/
==========================================

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