AMBER Archive (2003)

Subject: Re: mm_gbsa question

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Tue May 27 2003 - 20:40:36 CDT

Javier Cuervo wrote:
>
> Dear amber users,
>
> I am trying to run a mm_gbsa calculation using the decomposition by
> residue scheme. I did generate succesfully the topology files and
> snapshops for complex, rec and ligand, but when I try running the energy
> calculation I got the following error :
>
> Can't use an undefined value as an ARRAY reference at
> /home/programs/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1234.
>
> (It seems to me is something related with MS card (??) )
>
> and the las thing written in the .log file is:
>
> =>> Reading files
> Reading 2kai-sta_com.all.out
> Reading 2kai-sta_rec.all.out
> Reading 2kai-sta_lig.all.out
> =>> Treat special parameters
>
> and not "_statistics.out" file is written and nothing (but MM GB MS) is
> written in the "_all.out" files.
>

...

>
> Can anybody please tell me what I am doing wrong?

I would guess that sander is not running correctly although I don't see
an error in your mm_pbsa.in file at the moment. Comment the line "unlink
$sanout;" in "sub calc_MM_GB_SAS" in mm_pbsa.pl and rerun mm_pbsa.pl for
some of the snapshots. You should get the output file of sander, which
might help you. If not, let me know again.

Best regards

Holger

>
> I apologize for such big e-mail
>
> Regards
>
> Javier Cuervo
> Graduate Student
> Computational Sciences Research Center
> San Diego State University 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++