On Wed, Nov 18, 2015 at 6:38 PM, Mohammad Salem <mohammad.alaraby.gmail.com>
wrote:
> Thanks professor. I will try it in serial and see…
>
> The system is 226 amino acids in a cage of solvent. For doing it “by
> hand”, can you give me suggestions for where the procedure is explained?
>
The description is pretty simple. Normal modes are calculated from the
Hessian computed from a local minimum. So the steps are:
1. Minimize each snapshot, making sure to get very close to a local minimum
(it needs to be a lot closer to a local minimum than what you typically do
to prepare for MD). MMPBSA.py uses the xmin minimizer (this is described
in the manual).
2. Use a nab program to compute the Hessian and, from that, the normal
modes.
You can do both of the above two steps in a single nab program (see
mmpbsa_entropy.nab inside $AMBERHOME/AmberTools/src/mmpbsa_py for an
example).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Nov 18 2015 - 19:00:04 PST
