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

From: priya priya <>
Date: Fri, 6 Jul 2007 07:58:28 +0100 (BST)

Thank you for your suggestions.

Carlos Simmerling <> wrote: make the no-water prmtop the same way that you made your original prmtop.
I can't help with that since you did it yourself.

On 7/5/07, priya priya <> wrote: no-water.prmtop file is not created in this command.then how can one do that
for energy analysis i can use the test/trajene.

Carlos Simmerling <> wrote:

On 7/5/07, priya priya <> wrote: I am not able to understand what exactly you are saying.
lets me say in my words,
>From the Md run i have final mdcrd and rst files, using them i create a pdb file using ambpdb command and then make prmtop file using leap. Using this prmtop file i will remove water molcules using the ptraj >strip (water): command.
no, you use the original prmtop to read the old mdcrd and strip water

trajin mdcrd
strip :WAT
trajout nowat.mdcrd

for the energy analysis, there is an example in test/trajene that you can follow.
use the no-water prmtop with the no-water mdcrd file.

then how can i write a new mdcrd file from this and how to use sander command.
Sorry if i am asking the very basic step.

Carlos Simmerling < > wrote: 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,

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 - 06:07:35 PDT
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