AMBER Archive (2009)

Subject: Re: [AMBER] Fix the local structure as a rigid body

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jun 16 2009 - 08:15:12 CDT


it's better to apply strong positional restraints (see the ntr option in the
manual) unless you really need the coordinates not to change at all. with
restraints and a force constant of 10 to 100, the motion will be very small.

On Tue, Jun 16, 2009 at 9:11 AM, Yunjie Zhao <yjzhao.wh_at_gmail.com> wrote:

> Dear Amber users,
>
> Using Amber 9, I am trying to do molecular simulations with GB implicit
> solvent model. The PDB file has 28 residues. I want to fix the local
> structure (such as 15 to 23) as a rigid body when I do the molecular
> simulations.
>
> I do not know how to do this, can someone help me to figure it out? Any
> response will be appreciated.
>
> Thanks!
> Yunjie Zhao
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber