AMBER Archive (2005)

Subject: Re: AMBER: Multiple dihedral restraints (follow up)

From: M. L. Dodson (bdodson_at_scms.utmb.edu)
Date: Thu Feb 03 2005 - 14:07:11 CST

On Wednesday 02 February 2005 01:04 pm, David A. Case wrote:
> On Wed, Feb 02, 2005, Joseph Fernandez wrote:
>
> > I would like to add three dihedral restraints. Each
> > point of the dihedral angle is defined by a group of
> > atoms, rather than one atom. So for dihedral A-B-C-D,
> > A would be a group of atoms, B would be another group
> > of atoms, and so on...
>
> This sort of restraint is not provided in Amber. Only distance restraints
> can refer to "groups" of atoms, rather than individual atoms.
>
> ...dac

Hope it is appropriate to post this to the list. I'd like to
suggest the inclusion of this capability (very useful for umbrella
sampling) in the next version. Even better would be the ability
to restrain arbitrary atom groups using arbitrary functions, e.g.,
linear combinations of distances. Maybe by linking in an user
written function or subroutine conforming to a specific API? (I
do realize this might explode the support requirements.)

Bud Dodson 

-- 
M. L. Dodson                                bdodson_at_scms.utmb.edu
409-772-2178                                FAX: 409-747-8608

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