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
--
========================================
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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