[AMBER] trouble with mmpbsa.py

From: Chris Chris <alpharecept.yahoo.com>
Date: Fri, 18 Mar 2011 09:44:08 -0700 (PDT)

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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Received on Fri Mar 18 2011 - 10:00:02 PDT
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