VMD-L Mailing List

From: Itamar Kass (itamar.kass_at_gmail.com)
Date: Tue Feb 09 2010 - 05:15:27 CST

Hi all,

After doing some MD with GROMACS, I got PDB files and now I wish to
find Hbonds in my system. I was very happy to find a GUI plugin. So
before start working, I just have few question about the option and
the output.

1. I enter both selection 1 and 2, which allow me to chose at the
"Calculate detailed info foe" field between none, All bonds, Residue
pairs and Unique hbonds. I am not sure what is the meaning of each
option.

2. On the report I get Occupancies - what is the meaning of occupancy
different then 100 for one fame - meaning a static structure.

Cheers,
Itamar

===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar dot kass at med dot monash dot edu dot au
============================================