Re: regarding protein-protein interaction

From: Benjamin Bouvier (
Date: Fri Jun 05 2009 - 03:50:21 CDT

On Fri, 05 Jun 2009 09:51:37 +0200, prasun kumar <>

> Dear all
> I am trying to study protein-protein interaction using NAMD & CHARMM
> forcefield.
> Steps I am following are:
> 1. two proteins are placed at a distance of 10 angstrom to each other
> 2. minimized in vacuum
> 3. solvated in water and ionized
> 4. Minimization was done again
> 5. I have done the equlibration also
> 6. 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.
> 7. what should I do for it????????

Your equilibration was not careful enough. Start with a short constant-V
run, and play around with the langevinPistonPeriod and Decay parameters
when going to constant P.

> 8. I have studied that two proteins are interacting to each other(its
> proved in wetlab)
> 9. while doing dynamics the two proteins are not seems to coming
> towards
> each other

All-atom MD is probably not the best way to simulate 3D diffusion, because
of the timescales associated with it. You'll have to simulate a very long
time to see the complex forming, and the complex structure will depend
quite a bit on the starting position for the two partners -- ie, you might
not get what you expect. Brownian dynamics, evt. combined with
coarse-graining would be a better option IMO to get meaningful sampling.

> 10. I want to know whether I should "*tclforces on*" or not........

No, unless you want to bias your simulation (eg, by forcing the two
partners to meet along some coordinate). That's far from trivial though.

> Thanx in advance
> with regards
> Prasun kumar

Benjamin Bouvier
Structural Bioinformatics
IBCP Lyon - UMR 5086 CNRS
7, passage du Vercors
Tel: +33(0)4-37-65-29-44

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