Re: [AMBER] trouble with mmpbsa.py

From: Bill Miller III <brmilleriii.gmail.com>
Date: Fri, 18 Mar 2011 12:50:17 -0400

Since the ligand residues are not sequential, MMPBSA.py will not be able to
guess the proper residue numbers, so you will need to specify these by hand
using the receptor_mask and ligand_mask variables in the MMPBSA.py input
file.

-Bill

On Fri, Mar 18, 2011 at 12:44 PM, Chris Chris <alpharecept.yahoo.com> wrote:

> I am trying to perform mmpbsa analysis using the python version of the
> program
> on the complex in the attachment but have been unable to do so.
>
> As can be seen in the complex scematic, the ligand and receptor are not
> sequentially numbered. I thought this might be a problem so when I made the
> topology files, I kept the numbering as it was in the original pdb which
> was
> used to make the topology files in xleap.
>
>
> This was to no avail. Can anyone tell me what is going on here? Do I have
> to
> specify the residues in my .in file (see attached)?
>
> Thanks for any advice, I have also attached the .err and .out files as well
>
>
>
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>


-- 
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Mar 18 2011 - 10:00:05 PDT
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