On Tue, Mar 24, 2015 at 3:31 AM, Subrata Paul <paul.subrata34.gmail.com>
wrote:
> Dear
> Amber User,
>
> I have simulated a protein-urea-water system in AMBER12. Can we calculate
> the vdw energy and electrostatic energy for water and urea around the
> protein separately?
> any hints ?
>
​You can strip out the water using cpptraj and compute the energy of each
snapshot (using sander with imin=5). This will represent the urea-urea,
protein-protein, and protein-urea interactions. Then strip out the urea
and compute the energy of each snapshot​. This will represent the
water-water, protein-protein, and protein-water interactions.
Alternatively, the "energy" action in cpptraj will let you compute these
kinds of interactions, but it is a very simplistic sum-over-pairs energy
calculation, so you can't use PME or the dispersion correction (to my
knowledge) to correct for cutoff effects.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 24 2015 - 07:00:03 PDT
