AMBER Archive (2004)

Subject: Re: AMBER: problem with MM/PBSA

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed May 05 2004 - 05:14:47 CDT

Itziar Maestre Asenjo schrieb:
>
> Dear amber users
>
> I am trying to do a MM/PBSA calculations with AMBER7 using the option
> PB=1 but at the end of the calculations I have PBCAL=0, what it means
> that this energy term hasn't been calculated.
> I guess that the problem could be in the convertion between the crd file
> to the pdb file because I have done a single delphi calculation using
> the same file.crg and file.siz and I get right results.
> Furthermore, during the MM/PBSA run appears a temporary file fort13
> which corresponds to the pdb file in delphi
> Can someone explain me how the MM/PBSA makes this convertion between crd
> and pdb file?

The conversion is done in the routine generate_pdb in the file
mm_pbsa_calceneent.pl by calling "ambpdb" from the Amber suite.
Afterwards, naming of hydrogen is changed such that leading numbers are
put at the end of the hydrogen atom name.

> Does anybody know which one is the problem?

Which delphi version are you using? mm_pbsa has been tested on delphi
II. You might want to comment the line "unlink $delphiout;" in
mm_pbsa_calceneent.pl which will give you the delphi output file.

Best regards

Holger

>
> Thank you in adavance for any suggestion
>
> Itziar
>
> -----------------------------------------------------------------------
> 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

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

Tel.:  (+49) 69-798-29411; 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