From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Oct 19 2006 - 11:04:37 CDT
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
>>
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