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

From: Carlos Simmerling <>
Date: Thu, 5 Jul 2007 11:25:42 -0400

the easiest way is to do what I suggested, make a new prmtop in
leap and then use ptraj to strip the water and write a new mdcrd file.
then you can use sander to read in this trajectory with the imin=5
option and it will write energy for each frame. check page 90 of the
amber9 manual but note that the input trajectory is specified with -x,
not -y.

On 7/5/07, priya priya <> wrote:
> Hi,
> 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,
> Regards
> priya
> *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!
> > Regards
> ------------------------------
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Received on Sun Jul 08 2007 - 06:07:25 PDT
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