[gmx-users] gold-S simulation

[Justin Lemkul]

On 12/16/12 1:11 PM, francesco oteri wrote:
> Hi fatemeh,
> thank you for the references. Regarding your problem, what does it means
> you don't see any interaction?
> Is it possible it is just a problem of the visualization software. To be
> sure, you could monitor the distance
> between any S atom and the Au atom to which it is supposed to be bound. If
> the distance is stable around
> the equilibrium value you can say that the interaction is still present
>

In addition, if one is expecting some sort of covalent association, it must be 
defined in the topology.  This will not be true in the case of protein-Au 
interactions unless one makes appropriate entries in specbond.dat, similar to 
heme, or manual addition.  Bonded parameters are useless unless there is a bond :)

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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