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

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 1 Nov 2015 05:52:20 -0500

On Sat, Oct 31, 2015 at 1:21 PM, Gerald Monard <
Gerald.Monard.univ-lorraine.fr> wrote:

> As a follow-up, I can partially solve the problem using "iat":
> # d2
> &rst iat = 11, 48, r0 = 3.2, k0 = 0., /
> # d3
> &rst iat = 48, 49, r0 = 3.2, k0 = 0., /
> # d4
> &rst iat = 49, 16, r0 = 3.2, k0 = 0., /
> # d2-(d3-d4)
> &rst restraint = "coordinate(distance( :1.C :3.O ), 1.0, distance(
> :3.O :3.H1 ), -1.0, distance( :3.H1 :2.OP2 ), 1.0 )", r0 = 3.2, k0 =
> 0., /
>

​What happens if you use the "iat" approach here as well? I've often
observed rather funny behavior with the "natural language" restraints, and
there are a number of peculiar things about that code (for instance -- it
doesn't use the standard mask parser, it implements its own highly limited
version).

​​
> But I still can't add multiple "&rst restraint=[...]" commands.
> ​​
> I haven't seen such restriction in the manual, but may be I haven't
> ​​
> search correctly.
>

​There shouldn't be such a restriction, but I don't know that the code is
that well-tested (and it's quite complex as well).

All the best,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Nov 01 2015 - 03:00:03 PST
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