AMBER Archive (2005)

Subject: Re: AMBER: restraint only for Z cartegian coordinate?

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Tue Feb 22 2005 - 10:02:31 CST

the current sander version uses the same weight for the X, Y and Z
coordinates.
it would be very easy to modify the code to do what you want- look at
the xconst() subroutine in ene.f. you might start out by setting wx and
wy to zero,
but you'll need to test this out to make sure it is what you want to do.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Jaroslav Hanus wrote:

> I would like to know, whether there is a way to restrain the motion of
> some atoms only in one of its cartegian coordinates, for example to
> restrain only the z component and leave the x an y free (to keep some
> atoms in a predefined plane). From the manual it seemed to me that in
> principle it can be possible, but I did not find a way how to do this.
> Manual for Amber 8, page 101:
> RESTRAINT_WT: The weight (inkcal/mol−Å 2)for the positional
> restraints. The restraint is of the formk(∆x) 2, where k is the value
> given by this variable, and∆x is the difference between one of the
> Cartesian coordinates of a restrained atom and its reference position.
> There is a term like this for each Cartesian coordinate of each
> restrainted atom.
> thanks, sincerely
>
> Jaroslav
>
>
> ***************************************************************
> Jaroslav Hanus
> CERMAV
> Centre de Recherches sur les Macromolécules Végétales
> BP 53 38041 Grenoble Cedex 9 France
>
> Tel 33 (0)4 76 03 76 49
> Fax 33 (0)4 76 54 72 03
>
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