AMBER Archive (2008)

Subject: Re: AMBER: mmpbsa

From: Hannes Kopitz (Hannes.Kopitz_at_gmx.de)
Date: Tue Sep 02 2008 - 13:15:47 CDT

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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