Re: [AMBER] Need Help regarding Energy Calculation

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 18 Jan 2016 10:06:54 -0500

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> 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
> Mob:
> 8017650842
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Received on Mon Jan 18 2016 - 07:30:03 PST