I notice that MMPBSA would strip all the WAT including the important crystal water molequle. So I modified its name
to H2O and treated it as a ligand.
Now I find a convenient way to solve this problem. Just modify the name of the crystal water molequle in the topology files!
At 2012-06-01 21:22:54,"Jason Swails" <jason.swails.gmail.com> wrote:
>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 - 07:00:03 PDT
