Re: rigid protein

From: Anahita Tafvizi (atafvizi_at_fas.harvard.edu)
Date: Thu Oct 19 2006 - 10:50:01 CDT

so does the constraint in NAMD constrain the defined atoms to each other, or
to their positions in space? I mean with using this constrain will I still
be able to move the protein, but as a rigid body?

Thanks,
Anahita

On 10/19/06, L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu> wrote:

> 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
>
>

-- 
-- 
Anahita Tafvizi
PhD Candidate
Lyman 535
Physics Department
Harvard University
17 Oxford Street
Cambridge, MA 02138

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