AMBER Archive (2008)

Subject: RE: AMBER: mmpbsa

From: Henrik Öberg (henrikob_at_kth.se)
Date: Tue Sep 02 2008 - 09:18:56 CDT

I am using AMBER 9, so unfortunately mine is not included.
________________________________________
From: owner-amber_at_scripps.edu [owner-amber_at_scripps.edu] On Behalf Of Matthew Peterson [mpeterson_at_mitre.org]
Sent: Tuesday, September 02, 2008 3:57 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: mmpbsa

What version of AMBER are you using? There have been a few posts on
the reflector (mine included) regarding people having trouble with
mmpbsa in AMBER 10.

Matt

Matthew Peterson
The MITRE Corporation
mpeterson_at_mitre.org

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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