AMBER Archive (2004)

Subject: Re: AMBER: Pulling versus Distance Restraints

From: Furse, Kristina Elisabet (kristina.e.furse_at_vanderbilt.edu)
Date: Wed Sep 01 2004 - 12:08:49 CDT

You can use ifvari in your DISANG file to create a distance restraint that
varies with step number to gradually change the distance between two atoms over
the course of a simulation. Input section four of the manual.
good luck,
Kristina

Quoting Nhat-hang Duong <nhduong_at_rci.rutgers.edu>:

>
> Dear amber users,
>
> In amber8, is pulling two specific atoms of a molecule (e.g. a protein)
> to reasonable distance apart equivalent with restrainning the distance
> between these two atoms?
>
> If not, could anyone suggest a way to pull (or reposition) an atom in a
> molecule?
>
> Thanks,
> --Hang
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Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse_at_Vanderbilt.Edu
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