[AMBER] About mm-pbsa

From: 廖青华 <fantastic_0919.yahoo.com.cn>
Date: Thu, 19 Mar 2009 06:48:21 +0000

Dear Amber users,
I had  problems when I ran mm-pbsa of  three complexes which all had done the same MD simulation, but the results seemed different. The following are the output characters showed in the three complexes 

NO.1
[dock.localhost binding]$ mm_pbsa.pl mm_pbsa.in > mm_pbsa.log
molsurf: molsurf.c:1055: is_buried: Assertion `sarg1 >= 0.0' failed.
sh: line 1:  5441 已放弃?              /usr/local/amber9/exe/molsurf 1svg_com.pqr.27 0.0 >1svg_com.mslog.27
molsurf: molsurf.c:1055: is_buried: Assertion `sarg1 >= 0.0' failed.
sh: line 1:  8219 已放弃?              /usr/local/amber9/exe/molsurf 1svg_rec.pqr.46 0.0 >1svg_rec.mslog.46
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment

NO.2

[dock.localhost binding]$ mm_pbsa.pl mm_pbsa.in > mm_pbsa.log
molsurf: molsurf.c:1055: is_buried: Assertion `sarg1 >= 0.0' failed.
sh: line 1:  5447 已放弃?              /usr/local/amber9/exe/molsurf 1svh_com.pqr.19 0.0 >1svh_com.mslog.19
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
 
NO.3
 
[dock.localhost binding]$ mm_pbsa.pl mm_pbsa.in > mm_pbsa.log
vertex atom mismatch
       atom: 51
vertex atom: 49
vertex atom mismatch
       atom: 51
vertex atom: 49
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment

    The MD simulation of the four complexes were the same, but it seemed that the errors showed were different. And  I don't know the reason.  But finally it seemed that it ran mm-pbsa successfully, and I got the output files of statistics. I attached them, and you can have a check.
    Do these errors affect the results of the binding energy, and how to solve the problems? Thanks very much!

Best wishes!

Qinghua Liao from Tianjin University, China


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Received on Fri Mar 20 2009 - 01:13:15 PDT
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