Re: AMBER: How to extract energy of molecule from the system with explicit water molecules

From: priya priya <>
Date: Thu, 5 Jul 2007 16:10:23 +0100 (BST)

i want to extract the potential energy of the peptide without including the water molecules and not including the interaction of peptide with water.
I want it to calculate all the frames of the trajectory,

Carlos Simmerling <> wrote: do you mean just the internal energy, or also the interaction with
water? the latter is difficult in a periodic system. if you want just
the peptide energy, you can use ptraj to strip the water and then
make a prmtop of just the peptide without water. then you can
evaluate the energy of the peptide. if you want more specific suggestions
you'll need to make clear what you want- energy for a restart
file, or for all frames in the trajectory, energy with or without peptide:water
interaction, and so on.

On 7/5/07, priya priya <> wrote: Dear All

I am interested in extracting the energy of the molecule i.e peptide only from the output file that i obtained from running MD of that peptode in explicit solvent (water).

Please suggest me something!

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Received on Sun Jul 08 2007 - 06:07:24 PDT
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