AMBER Archive (2003)

Subject: Re: AMBER: fix some area

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Nov 07 2003 - 06:27:38 CST

I think you want positional restraints. Check the manual
for this, you'll use the ntr=1 setting. They are not
absolutely fixed (like a constraints) but they are restrained
using harmonic terms to stay near the positions in a reference structure
(which can be the initial structure).

  ----- Original Message -----
  From: Helios Chen
  To: amber_at_scripps.edu
  Sent: Friday, November 07, 2003 4:06 AM
  Subject: AMBER: fix some area

  Dear amber User, When I use sander to carry out energy minimization, has any program or methid to fix some area or some atoms(i.e. the relative position is constant each other in these fixed atoms)? Thanks a lot.

  Helios Chen

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