AMBER Archive (2003)

Subject: Re: AMBER: fix some area

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Sun Nov 09 2003 - 19:50:17 CST


you will need to be more specific.
you can specify ranges of residues,
so how you do it depends on which ones you
want to restrain. check the manual for GROUP
inputs.
  ----- Original Message -----
  From: Helios Chen
  To: amber_at_scripps.edu
  Sent: Sunday, November 09, 2003 8:21 PM
  Subject: Re: AMBER: fix some area

  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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