Re: [AMBER] Applying different restraints to different sets of atoms

From: David A Case <>
Date: Mon, 25 Jul 2016 10:50:47 -0600

On Mon, Jul 25, 2016, Dmitry Suplatov wrote:
> I want to simulate movement of one particular part of my protein (i.e.
> part1) while the rest of the protein (i.e., part2) should be left intact.
> For this I plan to apply positional restraints to the whole molecule and
> then during the relaxation period I want to gradually remove restraints
> from the part1 while retaining the restraints on the part2.

You can use the GROUP facility to define different restraint weights for
different groups of atoms. But I don't think you can vary the weight of
one group while leaving the other group's weight unchanged. You would need
to write a little script to run a series of jobs with varying input files.

...good luck...dac

AMBER mailing list
Received on Mon Jul 25 2016 - 10:00:03 PDT
Custom Search