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.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.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.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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Received on Mon Nov 10 2003 - 01:53:01 PST
