Thank you for your fast response David,
I see what you mean. I think i should find a way for grouping them first.
Then i can calculate free energies for each group through the
representatives (representative MD frames rather) of corresponding group.
Am i right ?
One more thing to ask. Should i use MMPBSA.py for this purpose ? If i have
for example 4 groups by some rule, can i treat them as
multiple (i don't know what this means though...) docking systems ?
thanks again million times
peker
On Wed, Nov 2, 2011 at 1:24 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Wed, Nov 02, 2011, peker milas wrote:
> >
> > I would like to ask whether there is a way of calculating free energies
> for
> > MD frames or not as a post-processing method. I read about MMPBSA.py but
> my
> > problem is not as complicated as described in documentation of MMPBSA. I
> > just want to calculate free energies of user specified residue(s) for
> each
> > MD frame. So, is this possible ?
>
> No. Free energy is an aggregate quantity the characterizes a thermodynamic
> state (or a collection of MD snapshots that is supposed to represent that
> state). It is not appropriate to think about the free energy of an
> individual
> snapshot. And, although it is possible to approximately decompose free
> energies on a residue-by-residue basis, such analysis always involves
> heuristic approximations.
>
> You might want to think about what you would do with the data you are
> asking
> about. Maybe some other quantity (which could be calculated) would serve
> your
> needs.
>
> ....dac
>
>
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Received on Wed Nov 02 2011 - 11:00:03 PDT
