very very thanks Jason
Can I use lie command in cpptraj of amber12 tools ?
On Tue, Mar 24, 2015 at 7:25 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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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>
--
*With Best RegardsSubrata PaulPhD StudentDept of Chemistry.IIT Guwahati*
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Received on Tue Mar 24 2015 - 23:00:02 PDT
