AMBER Archive (2008)

Subject: Re: AMBER: NTR Restraints

From: David A. Case (case_at_scripps.edu)
Date: Thu Mar 27 2008 - 15:17:31 CDT

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.

...dac

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