Re: AMBER: NTR Restraints

From: David A. Case <>
Date: Thu, 27 Mar 2008 13:17:31 -0700

On Tue, Mar 25, 2008, Daniel Smith wrote:
> I am doing a simulation of a channel protein with Na+ ions inside the
> channel. I would like to be able to restrain the Na+ atoms with one
> restraint weight (say 100 kcal/mol-A^2) and the CA carbons at a second
> restraint weight (say 20 kcal/mol-A^2). Is there a way to do this in AMBER?

I *think* you can do that by using the group input described in Appendix B:
see examples 1 or 2, but add the restraint weights.

As a practical matter, I doubt that you could see any difference between a
restaint of 100 and one of 20: both will effective prevent the relevent atoms
from moving.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Apr 18 2008 - 21:14:35 PDT
Custom Search