AMBER Archive (2001)

Subject: help for restrained minimization

From: xin.hu_at_ndsu.nodak.edu
Date: Fri Oct 26 2001 - 23:10:19 CDT

Hello,
I want to run the minimization with backbone restraint,
the following
is the input file I used, but I got an error that number
of atoms in
group is 0. I think the group definition must be wrong.
Would you
please tell me how to define the backbone group?
The second question is that i also want to constrain the
distance
beween two atoms (using NMR?), I appreciate very much
if
someone teach me how to do that.

the input file:

minimization with restrained main chain
 &cntrl
  imin = 1,
  maxcyc = 500,
  ncyc = 250,
  ntpr = 10,
  ntr = 1,
  ntb = 0,
  igb = 2,
  cut = 12.0,
 &end
Restrain the protein backbone atoms
5000.0
FIND
* * M *
SEARCH
RES 1 300
END
END

(how to restrain the distance?)

xin