Re: [AMBER] restraints with natural language

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 15 Aug 2014 15:33:22 -0400

On Fri, Aug 15, 2014 at 3:11 PM, Hugo Azurmendi <hazur_99.yahoo.com> wrote:

> I've tried to define restraints using natural language and failed.


​Error message? What program did you try this on? What version of Amber
are you using?

You didn't give us nearly enough information to help debug the problem.
 However, the natural language is not implemented in pmemd (nor will it be,
most likely). I would suggest sticking with the "iat" notation, as it is
far more frequently used (so more people can provide help with it).

Maybe someone can provide the correct syntax for the following example:
>
> # restraint = "torsion (:2.C2 :2.C3 :2.C4 :2.C5 )"
>

​I don't see anything inherently wrong with this. The example in the
manual uses [] instead of () to enclose the 4 atoms, but I don't use this
feature myself so I'm not sure what will work and what won't.


> &rst iat = 3, 7, 10, 14,
> r1 = 32.7, r2 = 42.7, r3 = 62.7, r4 = 72.7,
> rk2 = 10.0, rk3 = 10.0,
> &end
>
>
​HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 15 2014 - 13:00:02 PDT
Custom Search