On Thu, Jun 09, 2016, Sanjib Paul wrote:
> In my work I want to determine the energy of few selective water
> molecules of my system. For this purpose, can I follow energy
> decomposition technique of MMPBSA.py? If possible, may I know how should I
> proceed? Please help.
Take care to define terms carefully: water molecules exchange with each other
on a very rapid time scale, so the notion of the energy of an individual
water is a very slippery one. There are attempts to define such quantities,
but you need to think carefully about what use you are going to make of the
results. As always, look for existing studies that resemble those that you
wish to carry out, and see what was done.
MMPBSA won't help you: the first thing one does in such an analysis is to
remove all the water molecules. The GIST approach in cpptraj might be what
you looking for.
Consider also looking at geometric variables (such as the number of
hydrogen bonds), which can be readily computed and interpreted. (But, of
course, these are not energies.)
....dac
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Received on Thu Jun 09 2016 - 08:30:02 PDT
