AMBER Archive (2003)

Subject: AMBER: torsional restraints for groups of atoms

From: Anonymous (omeroueh_at_nd.edu)
Date: Sun Oct 19 2003 - 12:42:59 CDT

The question below was asked on the AMBER mailing list sometime ago, but I could
not find any reply to it. Is it currently possible to define torsional
restraints defined by four groups of atoms within sander?

>>I hope this goes through to the AMBER mailing list ... I have been
>>having problems posting ...
>>
>>
>>Question: Is it possible in sander to apply a torsional restraint on
>>center of mass of 4 groups? The manual describes (see page 140, v 7.0)
>>how a distance restraint can be applied between 2 COMs but does not say
>>anything about a torsional restraint.

Quoting "David A. Case" <case_at_scripps.edu>:

> On Fri, Oct 17, 2003, Qing Zhang wrote:
> >
> > I hope the belly option can be improved because it
> > will make computational cost much cheaper, especially
> > for large systems with small interesting parts, such
> > as ligand docking, protein tails. While restraints do
> > not reduce computational cost.
> >
>
> Note that the above statement is only true for pairwise potentials, and
> hence is not directly applicable to either PME or GB, which are the two
> main types of force field used in Amber.
>
> ..dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
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