I have created DNA and protein residues in Chimera for use in MD simulations. I would like to know about different ways to create a layer of gold atoms and a Au-S bond in PDB format so that it can be used for simulations. I would like to create a SAM of thiolated DNA on Au layer for the start.
What tools can I use ?
Suggestions are appreciated.
Dear Agnivo,
One possible solution is to first generate the desired layer of gold with some program, and then open it with VMD.
Then simply File --> Save Coordinates
In File Type, you should have already selected the PDB type, otherwise select it. Finally, save it. By this you will have the gold layer in the pdb format. Then I guess you can add this to the DNA/protein PDB files you already have.
In case you don't have VMD installed:
http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
Hope it helps!
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