On Thu, 2014-02-27 at 14:49 -0300, George Tzotzos wrote:
> Hi Jason,
>
> The files you requested to reproduce the problem are attached.
Oh man. I should have caught on to this earlier. You are keeping a
water molecule in your complex, but the default behavior for MMPBSA.py
is to strip _all_ solvent (and ions). You need to provide your own
"strip_mask" that will keep the water molecule you want as part of the
'solute'.
Since water molecules regularly exchange, you may have to do some
preprocessing of the trajectory file with cpptraj to make sure you get
the 'correct' water molecule in each frame.
Knowing what the error is now, no earlier version of MMPBSA.py will be
able to work around it. I'll see if I can add some sort of check for
this error, since it's fairly common.
Thanks,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 27 2014 - 11:30:02 PST
