From: Hidekazu WATANABE (evergreen_tow_at_yahoo.co.jp)
Date: Wed May 04 2005 - 16:40:23 CDT
Nice to meet you, all.
I'd like to simulate with fixing some of the atoms.
In the user's guide of the NAMD, the program reqires
the PDB file containing "fixed atom parameters".
http://www.ks.uiuc.edu/Research/namd/current/ug/node27.html
How to describe the fixed atom flags in the PDB files?
The contents of the usual PDB file are, for example, as follows:
========
ATOM 1 HA FOR 1 1.194 0.832 4.528 1.00 0.00
GRAA
ATOM 2 C FOR 1 1.812 1.528 3.962 1.00 0.00
GRAA
ATOM 3 O FOR 1 1.616 2.734 4.087 1.00 0.00
GRAA
ATOM 4 N VAL 2 2.761 1.038 3.158 1.00 0.00
GRAA
ATOM 5 HN VAL 2 2.895 0.053 3.091 1.00 0.00
GRAA
......
========
Is something added to write at the end of each line?
(I don't understand how to make it
because there are no more details or sampling data in the guide.)
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