From: Dong Luo (us917_at_yahoo.com)
Date: Tue Feb 09 2010 - 10:21:29 CST

Hi Itamar,

This options are defined by me. Try search the NAMD mailing list, they are all explained there.

Dong

----- Original Message ----
From: Itamar Kass <itamar.kass_at_gmail.com>
To: vmd-l_at_ks.uiuc.edu
Sent: Tue, February 9, 2010 6:15:27 AM
Subject: vmd-l: What occupancy at the Hbond plugin mean?

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
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| Monash University,
| Victoria 3800
| Australia
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| Tel: +61 3 9902 9376
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| E-mail: itamar dot kass at med dot monash dot edu dot au
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