Re: rigid protein

From: L. Michel Espinoza-Fonseca (
Date: Thu Oct 19 2006 - 10:14:21 CDT

Hi guys,

Yes, I think you can treat your protein as a rigid body with NAMD. A
natural question I would ask is "why do you want to keep your system
rigid, while performing molecular dynamics?". I'm asking you guys this
because you have to be careful when you analyze your results -you
could get completely meaningless results. Anyway, it's nothing of my
business :)

You can tell NAMD to keep the protein rigid by using the following lines:

fixedAtoms on
fixedAtomsForce on
fixedAtomsFile your_fixed_protein.pdb
fixedAtomsCol B

For that purpose, NAMD needs a pdb file containing the forces applied
to each atom in the protein to make it rigid. You can do that with VMD
by loading your protein and typing:

set all [atomselect top all]
$all set beta 1
$all writepdb your_fixed_protein.pdb

This will apply a force of 1kcal/mol to each atom. You can modify this
value based on your needs. The rest is straightforward.

I hope it helps. If you need further help, please let me know.


2006/10/19, Anahita Tafvizi <>:
> On 10/16/06, Mehdi Bagheri-Hamaneh <> wrote:
> Hi All,
> Is there a way to tell NAMD to treat a protein as a rigid body?
> Thank you in advance.
> Did someone answer to this question? I need to know the answer too, so I'll
> appreciate if you can put the answer up online for everyone.
> Thanks,
> Anahita
> --
> --
> Anahita Tafvizi
> PhD Candidate
> Lyman 535
> Physics Department
> Harvard University
> 17 Oxford Street
> Cambridge, MA 02138

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