This can definitely be done with MMPBSA.py. In fact, one of the test cases
for MMPBSA.py does only nmode calculations. When you tried excluding the &gb
and &pb flags did you also remember to include the &nmode flag?
The MMPBSA.py input file in
$AMBERHOME/AmberTools/test/mmpbsa_py/06_NAB_Nmode/ performs only an nmode
calculation.
MMPBSA input file for running nmode calculation
&general
keep_files=0, strip_mdcrd=0,
/
&nmode
nmode_igb=1, nmode_istrng=0.1,
/
Also, if you are not using AmberTools 1.5, then I strongly urge you to
upgrade since MMPBSA.py has undergone many improvements since its original
release with Amber 11.
I hope that helps.
-Bill
2011/5/12 Jesper Sørensen <lists.jsx.dk>
> Hi Amberlist,
>
> I am wondering if there is a way to get MMPBSA.py to ONLY calculate the
> entropy. I have in a separate calculation done the MM-PBSA calculations and
> now I am trying to get the entropy term included as well. It would be silly
> to have to do the entire calculation one more time.
>
> I tried just not including either the &gb or &pb flags, but then it
> defaults
> to &gb with standard settings. Is there a way to prevent this?
>
> Best,
> Jesper
>
>
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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 Thu May 12 2011 - 04:00:03 PDT
