On Fri, Oct 25, 2013 at 10:21 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Dear all,
>
> I set istrng=0.1 in MMPBSA input (0.1 M accoring to the AmberTools 13.0
> manual). According to the manual, PBSA uses mM as units .. Therefore in
> the PBSA input file created by MMPBSA.py I should see istrng = 100 ...
> However, in file _MMPBSA_pb.mdin I don't see this and istrng = 0.1 as in
> my MMPBSA.py.
>
> This is either a bug or some information is wrong in the manual or I am
> missing something.
>
> My AMBER tree is fully updated since last night.
>
I believe you are right when MMPBSA.py uses mmpbsa_py_energy to calculate
the energy. If you set use_sander=1 in the &general section, does the
resulting input file give the expected istrng?
Thanks for the report!
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 25 2013 - 08:30:02 PDT
