RE: About PDB file with fixed atom flags.

From: Michel Espinoza-Fonseca (
Date: Wed May 04 2005 - 17:07:13 CDT

The only thing you need is to fix some atoms, right? You can do it using
VMD and is really straightforward to do it. In the command line, after
you load your molecule, type the following:

set all [atomselect top all]
set fix [atomselect top "protein and name N"] (the name of your atom can
be HA, CA, O, C, etc., or if you want to fix; but if you want to fix the
backbone type:

set fix [atomselect top protein and backbone] )

after that, you have to type the following:

$all set beta 0
$fix set beta 1

And finally:

$all writepdb your_molecule_with_fixed_atoms.pdb

I guess it is what you want to know.


-----Original Message-----
From: [] On
Behalf Of Hidekazu WATANABE
Sent: Wednesday, May 04, 2005 4:40 PM
Subject: namd-l: About PDB file with fixed atom flags.

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".

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
ATOM 2 C FOR 1 1.812 1.528 3.962 1.00 0.00
ATOM 3 O FOR 1 1.616 2.734 4.087 1.00 0.00
ATOM 4 N VAL 2 2.761 1.038 3.158 1.00 0.00
ATOM 5 HN VAL 2 2.895 0.053 3.091 1.00 0.00
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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