AMBER: Pulling using restraintmask

From: Dirar Homouz <>
Date: Thu, 11 Dec 2008 14:30:00 -0600

Dear amber users,

I'm trying to pull a certain structure using restraintmask with a specified reference file.
I'm using the following input file

  imin = 0, ntb = 0,
  igb = 0, ntpr = 100, ntwx = 100,
  ntt = 3, gamma_ln = 1.0,
  tempi = 300.0, temp0 = 300.0
  nstlim = 100000, dt = 0.001,
  cut = 12.0
 with the following command

$AMBERHOME/exe/sander -O -i -o pull.out -c inpcrd -p prmtop -r rst -ref refc

The inpcrd file is different from the refc file. The last 24 atoms are shifted from their
initial positions.

When I run this simulation, it looks like my structure is being pulled to the coordinates in
the inpcrd file and that the refc coordinates are ignored.

Do you have any idea about what is going on?



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Received on Fri Dec 12 2008 - 01:19:49 PST
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