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
