Re: fixed residue

From: Joshua Adelman (
Date: Mon Jul 28 2008 - 23:16:41 CDT

Hi Rudra,

I'm guessing/hoping that you have taken a look at the user's manual on
this topic:

Assuming that you actually want to fix an atom position (rather than
just restraining it harmonically -- confusingly called 'constraint in
NAMD'), you want the following commands in your config script:
fixedAtoms on
fixedAtomsFile fixed.pdb // you can call it whatever you want, but
you want a pdb file with all of the atoms in your system including
fixedAtomsCol B // Although you can use any of the
options, but below I'll show using beta (B)

To create the appropriate pdb file you want to open up the tcl
interface and do something like the following:

set all [atomselect top "all"]
set sel [atomselect top "resname GLU"]

$all set beta 0.0
$sel set beta 1.0

$all writepdb fixed.pdb

If you do not understand the above commands, you need to go and look
at the various tcl scripting tutorials available online.


On Jul 28, 2008, at 8:49 PM, Rudra Banerjee wrote:

> As a beginner with NAMD, i am puzzelesd over how i can fix the atom
> position!
> i
> have Glu residue solvated in water. Now i want glutamines to be fixed.
> so if i use fixedAtoms tag on, what should i put in the
> fixedAtomfiles? the PDB file name of the gultamine?
> plz help
> --
> Rudra
> A bus station is where a bus stops. A train station is where a train
> stops. On my desk I have a work station.
> Please, if possible, don't send me MS Word or PowerPoint attachments
> Why?See:
> Unlimited freedom, unlimited storage. Get it now, on

Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley
Berkeley, CA 94720 USA

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