On Fri, Jun 1, 2012 at 6:03 AM, Cao Yang <muxiachuixue.163.com> wrote:
> Hi Jason,
> I must say I made a big mistake. I modified one of the crystal water's
> name from WAT to H2O in com_solv.pdb and saved a new
> topology file named com_solv.prmtop. This action loses the box information
> although the water molecules are still there.
>
Ah, you did this presumably to save that water molecule when running
MMPBSA.py? If you tell me why you did this, I may be able to suggest an
alternative solution so this is not necessary.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 01 2012 - 06:30:02 PDT
