AMBER Archive (2001)

Subject: Re: Define flexible residues during MD simulation

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Oct 23 2001 - 23:14:35 CDT

        Dear Amber users,
        Is here a way to define flexible residues group within a
        distance (like 20 A) of a mass center for MD simulation
        automatically? Or, you have to do that manually.

CUTRES in carnal generates the input for sander, e.g.:

  GROUP g1 (RES 1);
  CUTRES c1 g1 20.0;

for 20A from the center of mass of the 1st residue.

Bill Ross