Hii,
Thank you very much. I used GIST to calculate thermodynamic
properties of water molecules of a particular space of my interest. I got
energy of each water molecule. But in case of entropy I got negative
values. How is it possible to get a entropy value for a water molecule. I
followed the AMBER tutorial to carry out GIST and did what exactly said
there. Please, look into the matter.
Sanjib
On Thu, Jun 9, 2016 at 8:43 PM, David A Case <david.case.rutgers.edu> wrote:
> 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 Fri Jun 17 2016 - 03:30:03 PDT
