Simulation of Thiolated Biotin-Streptavidin on Gold

From: S.K. Ghosh (
Date: Tue May 20 2008 - 07:11:36 CDT

Dear users,

I am planning to set up the following simulation in NAMD. I would lke to
get your suggestion on whether this is feasible to do in NAMD.

I am trying to model the dynamics of biotin-streptavidin molecule where
biotin (thiolated) would remain attached to a Gold surface of a resonator
(QCM). So there would be a couple of layers of Au atoms, on top of it would
be a single layer of S atoms, on top of it Biotin, and attached to it one
strand of Straptavidin. I would like to investigate the forces in the
biotin-streptavidin bond as well as the S-Biotin and S-Au bond. Giving all
the atoms an acceleration I would be interested to find out which bond
gives in first, calculating the binding energy.

Is this possible to be set-up and run in NAMD?

Is giving a constant acceleration to all atoms feasible? Is it possible to
get the parameter files for Au-S, Biotin-S and Biotin-Streptavidin?

Your help would be precious in my work and would be much appreciated.

Thanks very much.

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