Re: [AMBER] Hello! Distance restraint problems in SANDER

From: David A Case <>
Date: Sat, 5 Nov 2016 20:35:33 -0400

On Sat, Nov 05, 2016, wrote:

> When optimising an nmr protein structure using SANDER, I wanted to
> stress one sets of distance restraints over others because I feel with
> confidence that this sets of restraints is more native like than others
> My question is : Is it possible to favour one sets of distance
> restraints over others, for example, setting the weight of one sets of
> distance rstrains higher than others in SANDER structure calculation
> programs.

Yes: the rk2 and rk3 variables control how rapidly the energy rises when
a distance restraint is violated. These can be different for each restraint.


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Received on Sat Nov 05 2016 - 18:00:02 PDT
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