AMBER Archive (2003)

Subject: Re: AMBER: fix some area

From: Helios Chen (p9890101_at_dec4000.cc.ncku.edu.tw)
Date: Sun Nov 09 2003 - 19:21:42 CST

Thanks for your reply, but how I write the restrain? For example, a protein included 100 amino acides, I want to restrain or fix residues of 20-30.
  ----- Original Message -----
  From: Carlos Simmerling
  To: amber_at_scripps.edu
  Sent: Friday, November 07, 2003 8:27 PM
  Subject: Re: AMBER: fix some area

  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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