Sir
Thanks for you suggestion. The study i undertake involves estimation of
effect of concentration of a compound to a protein.
I want to inquire if due to higher concentration of this compound there is
lack of water near the protein surface, which in turn leads to better
interaction between polar groups of the protein itself. I have some
experimental evidence to suggest this.
Hence the requirement of calculation of enthalpy. In fact i have MD
trajectories at different concentrations and i plan on studying the
variation.
Please suggest.
Thanks again.
Abhilash
On Sun, Dec 28, 2014 at 7:46 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Sun, Dec 28, 2014, Abhilash J wrote:
> >
> > I have a MD trajectory wit water, protein and one other compound. I am
> > interested in the enthalpy of the protein only over each frame the
> > trajectory.
> > I believe there must be some command in cpptraj or other AMBER modules
> > which can be of help to me. I tried finding it but am still unable to
> > locate it.
>
> The entire system has an enthalpy, which is close to its average energy in
> condensed phase, but this cannot be decomposed into a term for the "protein
> only", either experimentally or computationally, since the energy terms are
> not pairwise decomposable.
>
> You could strip the solvent and compute the average energy of the
> (gas-phase)
> protein. But this completely ignores the (very imporant) protein-solvent
> contribution (and the interaction of the protein with the other compound.)
> Furthermore, all molecular mechanics energies have an arbitrary zero, so
> only
> energy differences have any meaning.
>
> You should think carefully about exactly what you want to compute, and what
> use you would make of the resulting number.
>
> ...good luck....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 28 2014 - 08:00:02 PST
