Thanks Jason.
The water molecule that comprises part of the solute is numbered as residue 127
One of the default values of the strip_mask is is :WAT. How can one set the strip_mask for all water molecules except the one that is part of the solute (residue 127)?
Cheers
George
On Feb 27, 2014, at 4:08 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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 - 11:30:03 PST
