Hello Bill,
Firstly, I simply added hydrogens to the edge carbons to avoid the
number of bonds problem and I will see the antechamber result later(it
takes about 4 hours).
And I need to find out the reference about this periodic bonded
molecule according your suggestion.
Thank you.
Bongkeun Kim
Quoting Bill Ross <ross.cgl.ucsf.EDU>:
>> 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 - 15:00:06 PDT
