AMBER Archive (2004)

Subject: AMBER: Why the surface calculations sometimes fail?

From: hj zou (hjzou_at_iris3.simm.ac.cn)
Date: Wed Dec 08 2004 - 00:53:09 CST

Dear amber users:

I have some trouble running mm_pbsa.pl in Amber7:
It gave the following message before the final statistics script exit.

=>> Reading files
    Reading 1nrl_co_srl_com.all.out
    Entry 0 PB PB 0 exists -> overwriting
    WARNING: Missing GB for GB in 0 -> Taken from -1
    Entry 0 PB PB 1 exists -> overwriting
    Entry 0 PB PB 2 exists -> overwriting
    Entry 0 PB PB 3 exists -> overwriting
    Entry 0 PB PB 4 exists -> overwriting
    WARNING: Missing GB for GB in 4 -> Taken from 3
    WARNING: Missing SURF for MS in 4 -> Taken from 3
......
......

Some people had asked the same question,
Upon looking at the XXX_com.out
it seems to be something wrong with EGB field (nan)
and surface area (missing values) in several of the steps,
I commented cleanup commands in mm_pbsa.pl as told (http://amber.ch.ic.ac.uk/archive/200209/0171.html).
When checking the surface calculation log files:
Some snapshots indeed gave no surface area but a weird message instead.

NORMAL:
==> 1nrl_co_srl_com.mslog.1 <==

 5067 atoms read

WARNING: 3 cusps intersection: not trimmed yet
WARNING: 3 cusps intersection: not trimmed yet
WARNING: 3 cusps intersection: not trimmed yet
surface area = 15155.606

ERROR:
==> 1nrl_co_srl_com.mslog.10 <==

 5067 atoms read

WARNING: 3 cusps intersection: not trimmed yet
WARNING: 3 cusps intersection: not trimmed yet
two many interesecting cusps 6

What does the "two many interesecting cusps 6" mean?
Could somebody give an idea on this?
Any information about this would be greatly appreciated.

Best Regards!
Zheng.

===================================================
Mingyue Zheng
Drug Discovery and Design Center,SIMM
Chinese Academy of Sciences
#555 Rd.Zuchongzhi,Zhangjiang Hi-Tech. Park
Shanghai 201203, China
Tel: 86-21-50806600-1201(ext)
E-mail: myzheng_at_mail.shcnc.ac.cn;¡¡
        myzheng_at_iris3.simm.ac.cn;
===================================================£¬

        

   

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