AMBER Archive (2004)

Subject: Re: AMBER: problem with MM/PBSA

From: Holger Gohlke (
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 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 which will give you the delphi output file.

Best regards


> Thank you in adavance for any suggestion
> Itziar
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

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: URL: ++++++++++++++++++++++++++++++++++++++++++++++++++ ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to