From: Anahita Tafvizi (atafvizi_at_fas.harvard.edu)
Date: Thu Oct 19 2006 - 10:23:16 CDT
I need to treat my protein as a solid object but not fix it. I mean I want
to move it, but I don't want it to be unfold during the movement. with
the lines that you sent to us, the protein will be totally fixed. I wonder
if there is a way to constrain it to itself which means the protein atoms
will be fixed compared to each other.
On 10/19/06, L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu> wrote:
> 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 <atafvizi_at_fas.harvard.edu>:
> > On 10/16/06, Mehdi Bagheri-Hamaneh <mehdi.bagheri-hamaneh_at_case.edu>
> > 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
> > 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
-- -- Anahita Tafvizi PhD Candidate Lyman 535 Physics Department Harvard University 17 Oxford Street Cambridge, MA 02138
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