AMBER Archive (2008)

Subject: Re: AMBER: Problem with setting the NMR restraints

From: David A. Case (case_at_scripps.edu)
Date: Mon Aug 04 2008 - 10:26:51 CDT

On Mon, Aug 04, 2008, Alex Spasic wrote:
>
> I am trying to run a simulation of a small single chain DNA fragment
> using Amber 10 while holding fixed the torsion angle formed by the:
>
> (phosphate)i-(center of mass of sugar)i-(phosphate)i+1-(center of mass
> of sugar)i+1
>
> The restraint is defined by the following lines:
>
> # psps restraint
> &rst restraint = "torsion[:2_at_P,
> com(:2_at_C1',:2_at_C2',:2_at_C3',:2_at_C4',:2_at_O4'),:3_at_P,com(:3_at_C1',:3_at_C2',:3_at_C3',:3_at_C4',:3_at_O4')]",
> r1 = -180, r2 = -150.0, r3 = -150.0, r4 = -120.0,
> rk2 = 30.0, rk3 = 30.0
> /
>

As I remember (and from browsing briefly through he code) only distance
restraints can use the center of mass idea. It looks like the new format for
restraint input doesn't enforce this restriction. Matthew Seetin should look
at this and confirm (or not), but my intial guess is that you can't do what
you are trying here.

...dac

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