[gmx-users] Re: gold-S simulation

Justin Lemkul jalemkul at vt.edu
Mon Dec 17 22:17:18 CET 2012

On 12/17/12 4:01 PM, fatemeh ramezani wrote:
>   Dear Justin
> According to papers, I expect gold atom interacts with the sulfur atom of amino acid cysteine covalently. But in last email you said  in the case of protein-Au This will not be true to add these parameters
>   in topology file. Then in which file should I add the parameters between gold and sulfur?
> What do you suggest? How do I define for the program that can be established between these two atoms covalent bond ?

Bonds do not break and form in standard MD.  For that, you need QM or QM/MM type 

If there should be a bond between Cys and Au, you need to write that into the 
topology or use the specbond.dat mechanism.  pdb2gmx will not create bonds 
between Au and Cys otherwise.  The other modifications you have made, as far as 
I can tell, are fine.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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