Re: AMBER: fix some area

From: Carlos Simmerling <>
Date: Sun, 9 Nov 2003 20:50:17 -0500

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
  ----- Original Message -----
  From: Helios Chen
  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
    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
      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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Mon Nov 10 2003 - 01:53:01 PST
Custom Search