AMBER Archive (2007)

Subject: Re: AMBER: distance.restraint for two groups of atoms (center of mass)

From: David A. Case (case_at_scripps.edu)
Date: Sat May 12 2007 - 12:18:59 CDT

On Sat, May 12, 2007, Catein Catherine wrote:
>
> I am interest to do the distance restraint for two groups of atoms using
> their center of mass. It is the way I set the distance.restraint file.
> However, it did not work properly.

It would be more helpful if, instead of just saying "it did not work
properly", you said exactly what sort of result to obtained.

>
> # distance restrainst for group 1 (atom 122-150) and group 2 (atom 151 to
> 169)
>
> &rst iat=1,2, r1=0.0, r2=5.0, r3=5.0, r4=50.0, rk2 =30.0, rk3 = 30.,
> igr1(122/150), igr2(151/169), ir6=0 /

This is illegal syntax in the namelist command. "igr1" and "igr2" are arrays,
that have to be filled in, probably like this:

igr2 = 151,152,153,154,155,156,157,158,159,160,161,
       162,163,164,165,166,167,168,169,0

I don't think the "0" is required at the end, but it might be safer to put it
there.

...good luck...dac
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