AMBER Archive (2003)

Subject: Re: shake and belly

From: GUILLERMINA L ESTIU (gle10_at_psu.edu)
Date: Wed Jan 22 2003 - 12:47:30 CST

I am running a belly dynamics and it stops because the coordinates can't be
reset (displacement too large) and the I J atoms in the output are not included
in the belly. I do not completely understand this

On Wed, 22 Jan 2003 10:17:22 +0000, "David A. Case" wrote:

> On Tue, Jan 21, 2003, GUILLERMINA L ESTIU wrote:
> >
> > when running a belly dynamics, shake works on the moving residues or on all
> > the residues of the pdb file?
>
> I believe that sander removes all bonds in the frozen section as a
> preprocessing step. Hence, SHAKE doesn't "see" these, and does nothing
> to them.
>
> ..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
> ==================================================================
>
>
>

Dr Guillermina Estiu
Chemistry Department
Pennsylvania State University
PA 16802