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

From: Gerald Monard <Gerald.Monard.univ-lorraine.fr>
Date: Tue, 3 Nov 2015 19:47:00 +0100

On 11/03/2015 07:39 PM, Jason Swails wrote:
> 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
>

OK. I didn't read the doc carefully.
Then I guess that it means that the "coordinate(...)" keyword could be
dropped from the doc.

Thanks,

Gerald.


-- 
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Received on Tue Nov 03 2015 - 11:00:06 PST
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