AMBER Archive (2009)

Subject: Re: [AMBER] question of mm_pbsa

From: Ray Luo (ray.luo_at_uci.edu)
Date: Fri Jul 10 2009 - 11:47:12 CDT

Qinghua,

First thing first, have you patched the latest bugfix for mmpbsa,
bugfix.17 ...

Your output files seem to have all the data, but I noticed two redundant
entries for snapshot #1 in "2obd_com.all.out", indicating that you reran
the job without completely cleaning up the files. This may screw up the
statistical analysis.

So next time when you rerun it, please completely cleaning up the
directories/folders.

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

廖青华 wrote:
> Hi amber users,
>
> When I used mm_pbsa of amber10 to calculate the binding energy, everything went correctly, but finally I couldn't get the file of statistics.out. When I check the log file, I found that there were some warnings when reading the complex_all.out file, just like this:
>
> WARNING: Missing PB for PB in 0 -> Taken from -1
> WARNING: Missing PBCAV for PB in 0 -> Taken from -1
> WARNING: Missing PBDIS for PB in 0 -> Taken from -1
> WARNING: Missing SURF for MS in 0 -> Taken from -1
> WARNING: Missing PB for PB in 1 -> Taken from 0
> WARNING: Missing PBCAV for PB in 1 -> Taken from 0
> WARNING: Missing PBDIS for PB in 1 -> Taken from 0
> WARNING: Missing SURF for MS in 1 -> Taken from 0
> WARNING: Missing PBCAV for PB in 96 -> Taken from 95
> WARNING: Missing PBDIS for PB in 96 -> Taken from 95
> WARNING: Missing SURF for MS in 96 -> Taken from 95
>
> The attachment files are input and output files for you to check. Does anybody know the reasons for this situation and the solutions?
> Any resonse will be highly appreciated!
>
> Qinghua Liao
> fantastic_0919_at_yahoo.com.cn or fantasticqhl_at_yahoo.com
>
>
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