AMBER Archive (2008)

Subject: AMBER: restraintmask - reference file is not working

From: Dirar Homouz (dirar_at_hotmail.com)
Date: Tue Dec 16 2008 - 18:05:24 CST

Dear Amber users,

I'm trying to pull a certain structure using restraintmask from an initial structure
defined by the input file "inpcrd" to a final structure defined by reference file
"refc".
 I'm using the following input file

 ************************************************************
  &cntrl
   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
   ntr=1,
   ntrx=1,
   restraint_wt=100.0,
   restraintmask='@2276-2299',
  /
 ************************************************************
  with the following command

 $AMBERHOME/exe/sander -O -i pull.in -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.

The code runs fine. However, it doesn't move the structure to the
coordinates defined by the refc file. I'm not sure why is the refc file
is not recognized?

-Dirar

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