On Fri, 2014-03-07 at 12:32 +0530, Robin Jain wrote:
> Dear amber users,
> I am working on solvation of a organic molecule in methanol solvent using
> Amber12.
> Now i want to calculate the interaction energetics of organic molecule with
> methanol molecules. On surfing, I found that Amberlite is able to do it,
> but i do not know how can i use it. So i want procedure for using it to
> find out the interaction energetics. Please help me in this regard.
Amberlite cannot do this and I don't see any part of the manual that
suggests that it can.
You should also define what you mean by "interaction energetics" better.
Do you want the free energy of solvating your organic molecule in
methanol? If so and your organic molecule is small, you can use
softcore thermodynamic integration (there is a tutorial about it). Do
you just want the interaction energies postprocessed from a trajectory
you ran? In that case you can use cpptraj to create two systems: one
with just the methanol and another with just the organic molecules
(using the "strip" command with 'outprefix' to create corresponding
topology files). You can then compute the energy of each snapshot for
each trajectory and get an 'interaction' energy as the difference
between the energies of the whole system less the energies of the two
subsystems you created with cpptraj.
The approach you should take depends on what exactly you want to
compute. The suggestions that I made should provide sufficient detail
to get you started and hopefully point you to places in the manual and
tutorial to start looking.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 07 2014 - 06:00:05 PST
