Re: regarding protein-protein interaction

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri Jun 05 2009 - 03:19:43 CDT

Dear Prasun,

> Dear all
>
> I am trying to study protein-protein interaction using NAMD & CHARMM
> forcefield.
>
> Steps I am following are:
>
> two proteins are placed at a distance of 10 angstrom to each other
> minimized in vacuum
> solvated in water and ionized
> Minimization was done again
> I have done the equlibration also
> while doing dynamics ,volume is getting decreased and at last simulation is
> stopped saying fatal error related to the volume and asking to increase the
> margin.
> what should I do for it????????

How did you equilibrate? For how long time? Are you using an isotropic
piston? To go through the whole minimization, warming up and
equilibration process, I'll recommend you to take a look at the
available tutorials:

http://www.ks.uiuc.edu/Training/Tutorials/

> I have studied that two proteins are interacting to each other(its proved in
> wetlab)
> while doing dynamics the two proteins are not seems to coming towards each
> other

Keep in mind that most protein-protein interactions do not occur in
the nanosecond timescale, so it is very unlikely that you're going to
observe any native interactions.

If what you need is to get the structure of the complex, then you
should try to perform protein-protein docking first, then relax the
already formed complex using MD.

> I want to know whether I should "tclforces on" or not.......
>

I wouldn't recommend this, as I assume you don't know how the actual
complex looks like. There is a recent paper on protein-protein docking
using steered MD, though the method is not so trivial (Cuendet &
Michielin, Biophys. J., 2008, 95, 3575-3590)

Cheers,
Michel

> Thanx in advance
> with regards
> Prasun kumar
>
>

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