Re: [AMBER] restraints with natural language

From: Hugo Azurmendi <>
Date: Fri, 15 Aug 2014 13:06:53 -0700

Sorry I didn't give enough info. Using sander.MPI, Amber 14. I read the restraints from file, the error from output:

Error: Invalid atom or grouping specified in restraint.
restraint = "torsion (:2.C2 :2.C3 :2.C4 :2.C5 )"


where I just replaced 'iat = 3, 7, 10, 14,' with 'restraint = "torsion (:2.C2 :2.C3 :2.C4 :2.C5 )"' in the restraint file. I tried different variations with the same result. Of course, it works with 'iat' but it would be more convenient the other way.

On Friday, August 15, 2014 3:33 PM, Jason Swails <> wrote:

On Fri, Aug 15, 2014 at 3:11 PM, Hugo Azurmendi <> 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

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Aug 15 2014 - 13:30:04 PDT
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