AMBER Archive (2009)

Subject: Re: [AMBER] question of mm_pbsa

From: Hannes Kopitz (Hannes.Kopitz_at_gmx.de)
Date: Fri Jul 10 2009 - 04:36:44 CDT

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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