Ok, thanks. I will let you know if I get it to work!
Laura
Sent from my iPhone
> On Apr 17, 2015, at 8:00 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
>> 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 - 06:00:04 PDT
