AMBER Archive (2009)

Subject: AW: [AMBER] 2 restraints with different force constants

From: Aust, Susanne (saust_at_ipb-halle.de)
Date: Fri Jun 19 2009 - 06:51:21 CDT

Hello David,
thanks for your fast answer. How is the definition for the group input over
atom-numbers?
Because I will restrained only the benzimidazole-ring of my ligand + zinc and
the coordinating amino acids (over atom-ID's) the rest of the protein over
residue-numbers.
Thanks a lot!
Susanne

-----Ursprüngliche Nachricht-----
Von: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org]Im
Auftrag von David A. Case
Gesendet: 19 June 2009 13:41
An: AMBER Mailing List
Betreff: Re: [AMBER] 2 restraints with different force constants

On Fri, Jun 19, 2009, Aust, Susanne wrote:
>
> How I can combine these restraints with different force constants (active
> site = frozen (restrainted_wt=50) and rest of protein restrained_wt=10)?

I think if you use the group input (not the "mask" parameters, and
restraint_wt), you can just set different weights for different groups.
Run an experiment to see what happens.

Note that there will probably be a negligible difference between a restraint
weight of 50 and one of 10 -- both are quite strong and will essentially not
allow more than minimal movement.

...dac

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