On Thu, Apr 16, 2015 at 11:52 PM, Laura Tociu <ltociu.princeton.edu> wrote:
> Hi Jason,
>
> Thanks for the help. Truncating the trajectory and using ante-MMPBSA.py to
> generate topology files seems to work well. I could run MMPBSA.py just
> fine.
>
> However, I tried changing the mm_pbsa_createinput file but nothing changed
> after I recompiled. Namely I ran a short MMPBSA calculation on just a
> couple of frames and a small number of atoms. I used Nmode entropy
> calculation on the truncated trajectory before changing the code and I got
> the same value for the entropy as I got after changing the code and
> recompiling, which means no atoms were frozen Do you have any idea why
> this might be the case? Could it be that only when running regular mm_pbsa,
> the nmode input files are created with mm_pbsa_createinput, but when
> mmpbsa.py is used, the nmode input files are created using another code?
>
All of the perl modules (.pm files) correspond to the mm_pbsa.pl script.
Changing them will have no effect on MMPBSA.py's operation.
So for this particular application you will need to use mm_pbsa.pl
instead. Note that the topologies produced by ante-MMPBSA.py should still
work fine.
One caveat: you are entering uncharted waters for myself, so I will be able
to offer limited assistance (if any at all) with any future problems you
may encounter (and I suspect, though am not certain, that is true for
everyone else that regularly responds here as well).
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Apr 17 2015 - 05:30:02 PDT
