Re: [AMBER] MMPBSA.py error

From: Rasha Alqus <rasha.alqus.manchester.ac.uk>
Date: Thu, 24 Oct 2013 13:02:32 +0000

Dear Amber users,

The error occure during the GB calcualtion. I have attatched the files.
Am using ambertools12.

________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: 23 October 2013 12:40
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA.py error

On Wed, Oct 23, 2013 at 6:11 AM, Rasha Alqus
<rasha.alqus.manchester.ac.uk>wrote:

> ________________________________
> Dear Amber users,
>
>
>
> Am trying to calculate the binding energy using MMPBSA.py. When i ran the
> calculation for the first time i got an error saying (CalcError:
> /opt/gridware/apps/intel-12.0/amber12-intel-ib-compflags-axAVX/bin/mmpbsa_py_energy
> failed with prmtop receptor.top! Exiting. All files have been retained.). I
> used then ante-MMPBSA.py to produce the topology file for the dry complex,
> ligand and receptor, but when i ran the calculation i got the same error.
>

Please provide as much information as you can. For instance, this error
message could have occurred during GB calculations or (more likely) during
PB calculations. The debugging strategy strongly depends on when and where
this error occurred. Also, look in some of the calculation outputs to see
if there are any informative error messages (messages saying "There was an
error" are of limited help).

Also, what version of AmberTools are you using? AmberTools 12? 13? How
many updates have been applied?

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 24 2013 - 06:30:05 PDT
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