AMBER Archive (2009)

Subject: [AMBER] About mm-pbsa

From: 廖青华 (fantastic_0919_at_yahoo.com.cn)
Date: Thu Mar 19 2009 - 01:48:21 CDT


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_at_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_at_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_at_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 ___________________________________________________________ 好玩贺卡等你发,邮箱贺卡全新上线! http://card.mail.cn.yahoo.com/



_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber