AMBER Archive (2004)

Subject: Re: AMBER: Restrain or freeze molecule question?

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Jun 24 2004 - 10:39:58 CDT

you might also try the targeted MD option, which will apply
a restraint to the RMSD of selected atoms. you can then
have it fairly rigid but it can still rotate/translate.
carlos

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, June 24, 2004 11:24 AM
Subject: Re: AMBER: Restrain or freeze molecule question?

> On Thu, Jun 24, 2004, Guillaume Bollot wrote:
>
> > I would like to know if it's possible in AMBER7 to restrain internal
> > coordinate of the substrat with the possibility to move within antibody
> > site (like AutoDock)? In fact, I would like to keep the ab-initio
geometry
> > from Gaussian.
>
> You can restrain individual internal coordinates, using the "NMR"
restraints.
> If the ligand is simple enough, you could probably add enough of these to
keep
> it pretty rigid. There is no command to keep it exactly rigid, however.
>
> ...dac
>
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