On 04/03/2013 04:30 PM, Jason Swails wrote:
> Don't forget to modify "strip_mask" if you want to keep some water
> molecules. By default all waters (and ions) are stripped from the solvated
> trajectory.
>
> HTH,
> Jason
Hi Jason and Bill:
I think I found the problem:
the initial protein.pdb already have crystal water, and in the
initial rec.top file, it also contains crystal water. So if I didn't
specify them to be included in the MMPBSA step, they would be deleted so
that the following step is not consistent with initial rec.top file.
I re-generate the .top file, and it works very well now.
thanks again for kind helps.
best
Albert
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Received on Wed Apr 03 2013 - 08:00:04 PDT
