From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Oct 19 2006 - 13:12:53 CDT
I find this actually an interesting topic. Is it possible to apply NOE
restraints between two hydrogen atoms like with CHARMM?
Gianluca
On Thu, 19 Oct 2006, JC Gumbart wrote:
> There is a way to directly apply constraints to bonds (between any two atoms,
> not just covalently linked ones), angles, etc. You could use this to apply a
> few distance restraints between arbitrary atoms on, say, the edges of your
> protein that could effectively make it rigid.
>
> http://www.ks.uiuc.edu/Research/namd/2.6/ug/node34.html#SECTION000973
>
> On Oct 19, 2006, at 10:55 AM, Marcos Sotomayor wrote:
>
> >
> >I am afraid NAMD cannot treat proteins as rigid bodies easily. Both
> >fixedAtoms and constraints make reference to fixed points in space. If you
> >have one protein, then its OK (as Mark pointed out). However if you have many
> >proteins and you want to, lets say, see how they diffuse without worrying too
> >much about their internal motions, then those options are not useful.
> >
> >You could either put internal constraints using Tclforces (like virtual bonds
> >between different parts of the protein) or try to hack the Targeted MD code
> >so as to keep your protein within some RMSD from the original structure. All
> >these options, however, will not save you much computation time, which is
> >likely what you are looking for.
> >
> >Marcos
> >
> >
> >On Thu, 19 Oct 2006, L. Michel Espinoza-Fonseca 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
> > >
>
>
-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
+1 (206) 685 4435
+1 (206) 714 4303
http://biocroma.unizh.ch/gianluca/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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