AMBER Archive (2004)

Subject: Re: AMBER: questions about mmpbsa

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Fri Mar 05 2004 - 01:35:57 CST

>
> 2. In the output file, mmpbsa.out, I always find some warnings:
>
> Reading d3hvpMD_com.all.out
> WARNING: Missing GB for GB in 21 -> Taken from 20
> WARNING: Missing SURF for MS in 34 -> Taken from 33
> WARNING: Missing SURF for MS in 58 -> Taken from 57
> Reading d3hvpMD_rec.all.out
> Checking CALC
> WARNING: Missing SURF for MS in 58 -> Taken from 57
> Reading d3hvpMD_lig.all.out
> Checking CALC
> WARNING: Missing SURF for MS in 58 -> Taken from 57
> WARNING: Missing SURF for MS in 62 -> Taken from 61
> WARNING: Missing SURF for MS in 70 -> Taken from 69
>
> is it normal or something wrong?

It means that e.g. no surface area was found/calculated for the complex
snapshot 34. To get an idea as to what might have gone wrong here,
comment the line "unlink $mol;" in the subroutine calc_ms in mm_pbsa.pl
. Similarly, you may want to comment the other "unlink ..." lines in the
calc_... routines in mm_pbsa.pl.

>
> 3. Today, one of my jobs is "Exit 25", not "Done". I checked the output
> file, and found the job was stop at "Calc Delta" :
>
> Processing GB GBTOT
> Doing 1 GB GBSOL
> Doing 1 MM GAS
> Doing 1 GB GBSOL
> Doing 1 MM GAS
> Doing 1 GB GBSOL
> Doing 1 MM GAS
> =>> Calc delta
>
> Does anybody know what's the problem here?

Have a look in the xxx_{com,rec,lig}.all.out files and the output files
after commenting the "unlink ..." lines.

Best regards

Holger Gohlke

>
> Thank you so much
>
> All the best
>
> Shawn Hu
> Chem. Depart.
> Univ. of Memphis
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu 

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Juniorprofessur fuer Molekulare Bioinformatik

J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Germany                         

Tel.:  (+49) 69-798-29503; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.rz.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu