From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Oct 19 2006 - 10:38:33 CDT
Indeed, there is a way in which you can apply constraints to youf
protein. You can change this:
fixedAtoms on
fixedAtomsForce on
fixedAtomsFile your_fixed_protein.pdb
fixedAtomsCol B
By something like this:
constraints on
consRef your_restrained_protein.pdb
consKFile your_restrained_protein.pdb
consKCol B
and you'll follow the same procedure in VMD to tell NAMD which atoms
will be restrained:
set all [atomselect top all]
$all set beta 1
$all writepdb your_restrained_protein.pdb
As I mentioned before, you can play around with different values
(i.e., from 0.3 to 1) and see which one gives you the desired results.
You can also take a look to the NAMD manual for further information.
Cheers,
Michel
2006/10/19, Anahita Tafvizi <atafvizi_at_fas.harvard.edu>:
> Hi,
>
> 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.
>
> Thanks,
> anahita
>
>
>
> 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.
> >
> > Enjoy!
> > Michel
> >
> >
> > 2006/10/19, Anahita Tafvizi <atafvizi_at_fas.harvard.edu>:
> > > On 10/16/06, Mehdi Bagheri-Hamaneh < mehdi.bagheri-hamaneh_at_case.edu>
> 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
> >
> >
>
>
>
> --
> --
>
> Anahita Tafvizi
> PhD Candidate
> Lyman 535
> Physics Department
> Harvard University
> 17 Oxford Street
> Cambridge, MA 02138
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