Hi,
I am also interested in this question. Usually this is needed for FEP
calculations but unfortunately we dont have FEP implemented in amber. I will
ask about thermodynamic integration. When we do TI calculation, then can we
write interaction energy of ligand from its surrounding. I would
be interested to use amber for using Linear interaction energy approach for
free energy calculation. What i need from the AMBER simulation is, vdW
and electrostatic interaction energy of particular group of atoms (for whole
ligannd and may be some ions) in salivated protein ligand complex.
Please can anyone suggest the way to extract interaction energies in amber ?
..Sushil
On Tue, Oct 19, 2010 at 8:43 AM, balaji nagarajan
<balaji_sethu.hotmail.com>wrote:
>
> dear Amber 1
>
> I would like to know the interaction between the solvent and the
> solute is it possible to do in amber ?
>
> The Energy printed in amber is for the total , but i would like to know the
> interaction energies , how one can do this with amber ?
>
> regards
> balaji
>
>
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Received on Mon Oct 18 2010 - 21:30:02 PDT
