AMBER: extract protein energy from MD trajectory

From: Mikyung <>
Date: Tue, 10 Jul 2007 15:47:53 -0600

Hello amber users,

I tried to extract energy of protein from protein-sugar interaction MD
trajectory using imin=5.
As Carlos said, I used "-x" option to read the previous trajectory and
calculate energy for protein only.

What I did are:

1. MD simulation of protein-sugar in the gas phase
2. strip sugar from trajectory and save to new trajectory
(MDtraj_protein.x) using ptraj
3. create topology ( and coordinates (protein.crd) files
for protein only in xleap
4. load new trajectory using imin=5 and calculate energy

Here are input and command to run calculation:

      imin = 5, ntx = 1, maxcyc=1,
      scnb = 2.0, scee = 1.2,
      cut = 9999.0

sander -O -i -o proteinE.out -p -c protein.crd
-x MDtraj_protein.x

However, I don't get any output file.
There is nothing in proteinE.out file.
What is wrong with my input or command?

Is there anyone to have same problem and can you help me?


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Received on Wed Jul 11 2007 - 06:07:52 PDT
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