AMBER Archive (2008)

Subject: Re: RE: AMBER: mmpbsa

From: Hannes Kopitz (Hannes.Kopitz_at_gmx.de)
Date: Wed Sep 03 2008 - 04:15:19 CDT

Hi,

You need to provide the according prmtop as well as at least the mm_pbsa.in.
Additionally your log-file and outputs from sander, if present, would be helpful.

Cheers!
Hannes

-------- Original-Nachricht --------
> Datum: Wed, 3 Sep 2008 09:30:43 +0200
> Von: "Henrik Öberg" <henrikob_at_kth.se>
> An: "amber_at_scripps.edu" <amber_at_scripps.edu>
> Betreff: RE: AMBER: mmpbsa

> Hi again,
> the crd file is attached in this mail.
> Henrik
> ________________________________________
> From: owner-amber_at_scripps.edu [owner-amber_at_scripps.edu] On Behalf Of
> Hannes Kopitz [Hannes.Kopitz_at_gmx.de]
> Sent: Tuesday, September 02, 2008 8:15 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: mmpbsa
>
> Hi Henrik,
>
> If you provide some more information it should be possible to solve your
> problems.
> First of all, are there any outputs?
> For instance from sander. If so, please attach them.
> If not, it should be helpful to paste the whole contents of your
> mm_pbsa.in and of your log-file.
> If then the reason for your trouble still remains unclear to the
> community, you should attach the prmtop-files and at least one crd-file per COM, REC
> and LIG.
>
> Cheers!
> Hannes
>
>
> On Sep 2, 2008, at 7:36 AM, Henrik Öberg wrote:
>
> > Hi AMBER users,
> > I have a problem calculating the binding free energy of my complex.
> > After generating the snapshots using mmpbsa.pl, which I think works
> > just fine, the problem presents itself when I start the binding
> > energy calculations. Directly after executing the folllowing command:
> > $AMBERHOME/exe/mm_pbsa.pl binding_energy_13.mmpbsa >
> > binding_energy_13.log,
> > where binding_energy_13.mmpbsa holds the input specifications, I
> > get an error message just telling me the run was not successfull,
> > which is not very informative..
> > Has anyone encountered a similar problem?
> > Thankful for any help!
> > Cheers
> > Henrik Oberg,
> > KTH Sweden
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