Thank you Jason for the suggestion.
On Monday 18 January 2016, Jason Swails <jason.swails.gmail.com> wrote:
> Try using MMPBSA.py. It handles removing explicit water and calculating
> energies using an implicit solvent model.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
> > On Jan 18, 2016, at 6:57 AM, Saikat Dutta chowdhury <
> pbr322.dutta.gmail.com <javascript:;>> wrote:
> >
> > Dear Amber Users,
> >
> > I have performed an explicit solvent simulation of a peptide molecule and
> > saved the resulting trajectory.
> > I want to calculate the energy of each conformations in the trajectory.
> For
> > that I consulted amber14 manual and found out that there is a way
> mentioned
> > in section 17.6.1. But I donot know how to calculate the energy without
> > considering the explicit water.
> >
> > Could anyone suggest How to calculate energy of the conformations without
> > considering the explicit water environment
> >
> > with regards,
> > --
> > Saikat Dutta Chowdhury
> > Email: pbr322.dutta.gmail.com <javascript:;>
> > Mob:
> > 8017650842
> > _______________________________________________
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> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jan 18 2016 - 20:00:03 PST
