Re: AMBER: PBCAL=0. Problems in MM/PBSA

From: Holger Gohlke <>
Date: Fri, 14 Jan 2005 08:31:45 +0100

Dear Javier,

> I have a problem with my MM/PBSA calculations.
> When I do the calculation using MM/GBSA (without Delphi), I obtain a value of
> GB that it is not 0.0. So, the MM/GBSA calculation goes right.
> Nevertheless, when I run a MM/PBSA using AMBER7 and Delphi, I obtain the value
> of PBCAL is 0.0.
> The delphi.log files that I obtain are like this:
> opening formatted file:fort.13
> number of atoms read in = 0
> exiting due to non-existence of atom file
> _______________________________________________
> I have read Delphi manuals and I know that fort.13 is a file with pdb format.
> I've read in AMBER7 manual about mm/pbsa and it doesn't talk about we have to
> use a pdb file in should generate a pdb file "on the fly" prior to the delphi
calculation, which is then linked to the name fort.13. See the
generate_pdb and calc_PB routines in This conversion is done
using ambpdb from the AMBER suite. As a test, try to convert a snapshot
via ambpdb by hand and see whether any errors occur in this step.

Best regards


> Maybe there are some bugs in the I have (ver. 1/16/2002 ). Do you
> know if there is a new version of ?
> If someone can help me, I accept any suggestion.
> Thanks in advance,
> Xavi
> Javier Perez
> Grup de Química Orgànica Estructural
> Departament de Química
> Universitat Autònoma de Barcelona
> 08193 Bellaterra-Espanya
> Lab.: C7-455
> Tel.: +34 935811266
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Received on Fri Jan 14 2005 - 07:53:00 PST
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