Re: Simulation of Thiolated Biotin-Streptavidin on Gold

From: S.K. Ghosh (
Date: Wed May 21 2008 - 08:16:24 CDT

Dear NAMD users,

Thanks for your all yesterday's suggestions. As Axel pointed out that even
5 picosec of simulation with organometallic contacts would need more than a
month simulation, and my interest is of a few nanosecs, I would rather
start with only biotin-streptavidin complex. The biotin will be fixed and
force will be applied to streptavidin (similar to an AFM exp). From my
reading of the tutorial this seems to be implementable in NAMD. I would
appreciate your views on this.

I have got the complex (PDB code: 1swe) from Preotein Data Bank. Could you
please let me know where I could get the psf and parameter files from.

This would be very helpful indeed.


On May 20 2008, Axel Kohlmeyer wrote:

>On Tue, 20 May 2008, S.K. Ghosh wrote:
>SKG> Dear users,
>dear sourav,
> SKG> I am planning to set up the following simulation in NAMD. I would
> lke to SKG> get your suggestion on whether this is feasible to do in
> NAMD. SKG> SKG> I am trying to model the dynamics of biotin-streptavidin
> molecule where SKG> biotin (thiolated) would remain attached to a Gold
> surface of a resonator SKG> (QCM). So there would be a couple of layers
> of Au atoms, on top of it would SKG> be a single layer of S atoms, on top
> of it Biotin, and attached to it one
>actually the structure of thiols on gold is not that trivial.
>please see for example Mazzarello et al. PRL 98, 016102 (2007).
> SKG> strand of Straptavidin. I would like to investigate the forces in
> the SKG> biotin-streptavidin bond as well as the S-Biotin and S-Au bond.
> Giving all SKG> the atoms an acceleration I would be interested to find
> out which bond SKG> gives in first, calculating the binding energy.
>please note that in typical classical force fields bonds are
>represented by harmonic potentials, i.e. they cannot break
>and are only realistic near the equilibrium distance.
>you would have to use a different functional form. but even then
>i doubt that a classical potential is sufficient to describe the
>behavior. see for example Krueger et al., PRL 89, 186402 (2002)
>and Konopka et al., JACS 126, 1203 (2004).
>you would have to do a quite complicated and time consuming
>QM/MM simulation, which would probably also need you to adjust
>and existing QM/MM code to be able to handle a metallic surface
>system. all qm/mm "bio"-capable codes i know (and i've seen quite
>a few over the last years) assume a small, isolated QM system.
> SKG> Is this possible to be set-up and run in NAMD? SKG> SKG> Is giving a
> constant acceleration to all atoms feasible? Is it possible to
>i'd say that the constant acceleration will be the least of your
>problems. have you made a reality check? how fast on the atomic scale
>does your system move in the experiment? what is the period of the
> axel.
>p.s.: just to give you an estimate... a 5 picosecond DFT trajectory
>of 16 hexane thiols on a 4-layer gold slab takes about a full month
>running 24/7 on one rack of a bluegene/l (2048 cpus) (=1.5 mio cpu
>SKG> get the parameter files for Au-S, Biotin-S and Biotin-Streptavidin?
>SKG> Your help would be precious in my work and would be much appreciated.
>SKG> Thanks very much.
>SKG> Sourav

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