Re: [AMBER-Developers] [AMBER] &rst + distance + coordinate restraint

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 3 Nov 2015 13:39:38 -0500

On Tue, Nov 3, 2015 at 1:33 PM, Gerald Monard <
Gerald.Monard.univ-lorraine.fr> wrote:

>
>
> On 11/03/2015 07:14 PM, Jason Swails wrote:
> > ‚ÄčThere is nothing you can do with the "natural language" restraints that
> > you can't do with the iat, igr1-8, and rstwt variables to my knowledge.
> > Someone please correct me if I'm mistaken!
>
> From the Amber15 doc, the equation given for rstwt seems to concern
> only distances, not angles, or other "fancy" things (as Adrian said)
> that restrain+coordinate can give you. But may be I haven't understood
> everything from that chapter.
>
> Because there are not so many tests for the restraint keyword, may be we
> could start first by listing what works, what does not work or crashed
> and then decide whether there is room or need for improvement.
>

‚ÄčThat would be something. Can angles and torsions be used *with*
"coordinate" in natural language? Because *that* is something not
supported by iat/igr...

But I don't think that's the case -- here is what the manual says:

Within the "coordinate( )" keyword, the user must use 2 to 4 "distance( )"
keywords to define a
generalized distance coordinate restraint.

So it sounds like only 2 to 4 distances are supported by natural language
"coordinate", which is exactly what you can do through iat/rstwt...

All the best,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 03 2015 - 11:00:05 PST
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