AMBER Archive (2003)

Subject: Re: shake and belly

From: David A. Case (case_at_scripps.edu)
Date: Wed Jan 22 2003 - 12:17:22 CST

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
==================================================================