AMBER Archive (2009)

Subject: 回复： [AMBER] question of mm_pbsa

From: 廖青华 (fantastic_0919_at_yahoo.com.cn)
Date: Fri Jul 10 2009 - 20:22:25 CDT

Hi Prof. Hannes Kopitz,
I followed your suggestion to run mm_pbsa_statistics.pl manually after delete the redundant lines in the 2obd_com.all.out file. But I found that I still can't get the statistics.out file. It shows in the terminal like this:
 
=>> Reading input
=>> Reordering files
    Final order:
    1. 2obd_com.all.out: -
    2. 2obd_rec.all.out: -
    3. 2obd_lig.all.out: -
=>> Reading files
    Reading 2obd_com.all.out
    Reading 2obd_rec.all.out
    Checking consistency of CALC
 not foundGB

I don't know why not found GB, could you help me figure it out? Thanks!

All the best,

Qinghua Liao
fantastic_0919_at_yahoo.com.cn or fantasticqhl_at_yahoo.com

________________________________
发件人： Hannes Kopitz <Hannes.Kopitz_at_gmx.de>
收件人： AMBER Mailing List <amber_at_ambermd.org>
已发送： 2009/7/10(周五), 下午5:36:44
主题： Re: [AMBER] question of mm_pbsa

Dear Qinghua,

I guess the problem is that the MM part of the first snapshot occurs three times in the 2obd_com.all.out file. It should work if you delete the redundant lines in this file and run the mm_pbsa_statistics.pl script manually.

Cheers!
Hannes

-------- Original-Nachricht --------
> Datum: Fri, 10 Jul 2009 09:49:40 +0800 (CST)
> Von: "廖青华" <fantastic_0919_at_yahoo.com.cn>
> An: amber_at_ambermd.org
> Betreff: [AMBER] question of mm_pbsa

> 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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