> I built a single layer of graphite according to the crystal operation.
> And I tried to generate the parameter file for it with antechamber.
Normally one would build a small residue unit that could be
repeated to create the sheet, parameterize the residue with
antechamber, create a pdb with multiple such residues (and
ideally CONECT records for the bonds), and loadpdb. Without
CONECT records, one would need to add bonds between the residues
in leap, since it is designed to only auto-connect strands.
Graphite looks like a rather difficult case. I imagine that
the residue unit would be a smaller sheet, maybe with 9
rings (3x3), and that, if edge effects are of interest, for maximum
accuracy on charges one would want different such residues along
edges and in corners.
People have asked questions about modeling fullerenes before -
you might find useful references for this in the literature. I
speculate that a significant number of people modeling periodic
bonded structures like this may wind up using other programs.
Bill
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Received on Thu Oct 14 2010 - 15:00:05 PDT
