Re: rigid protein

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Thu Oct 19 2006 - 10:55:07 CDT

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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