On Thu, Aug 1, 2013 at 1:07 PM, Hunter Brown <bassoongoon.earthlink.net>wrote:
> Hello, I am trying to create files for MMPBSA.py free energy analysis. My
> complex topology file (stripped of water and ions) was created
> successfully, however when ante-mmpbsa.py moved on to work on the receptor
> (which I chose to be my protein structure) I got the following error. It
> seems odd to me that the complex would have no problems, and then fail to
> create the other files. I was just wondering what the problem might be? I
> hope this is specific enough.
>
> Creating receptor topology file by stripping !(.8587-48269) from
> 3foldposope2comp.prmtop
>
This seems like a strange ligand mask to be using. Your ligand is 40K
atoms?
Can you send me your prmtop and the ante-MMPBSA.py command you used?
Also make sure you are using an up-to-date AmberTools 13 installation. [[
$AMBERHOME/update_amber --version ]] should return AmberTools version
13.14.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 01 2013 - 11:30:03 PDT
