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
>
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--
++++++++++++++++++++++++++++++++++++++++++++++++++
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.bioinformatik.uni-frankfurt.de
URL: http://www.rz.uni-frankfurt.de/~hgohlke
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Received on Wed May 05 2004 - 12:53:00 PDT
