If your snapshots do not properly minimize, then they will not be included
in the nmode calculations. You should be able to fix this by adjusting the
convergence criteria (either tolerance or increasing the minimization
steps) in the MMPBSA.py input until all snapshots are able to be minimized.
The default minimization parameters will work for many, but not all
systems, and may need to be tweaked depending on the specifics of a system.
Good luck!
-Bill
On Fri, Jun 22, 2012 at 6:55 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> Hello All
>
> I am calculating entropy of protein - DNA complex. I have four complex,
> when I
> ran MMPBSA first time then for two complex I got WARNINGS:
> Not all of your snapshots minimized within tolerable limits for nmode
> though it is giving delta entropy calculation.
>
> When I ran MMPBSA second time for two above complexes, for one complex I
> didn't
> got any warning but for second complex I got again same warning.
>
> I am not getting whey getting warning again for one complex, will it affect
> calculated delta entropy during same run?
>
>
> Sangita Kachhap
> SRF
> BIC,IMTECH
> CHANDIGARH
>
> ______________________________________________________________________
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--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Jun 22 2012 - 11:30:03 PDT
