On Mon, Jun 17, 2013, dpiraner.caltech.edu wrote:
>
> I'm trying to obtain .top and .crd files for a graphene sheet using
> AMBERtools 1.4. I generated the graphene pdb file using VMD's nanotube
> builder plugin, and added terminal hydrogens using PyMOL. I then replaced
> the VMD atom names (C and H01) with what I believe to be the appropriate
> GAFF atom names: CA and HA. The structure was then used as an input for
> Antechamber, to be then loaded into tLEaP:
Sorry, but your input structure is way outside the area for which antechamber
could be expected to work. While you could technically think of your molecule
as "organic" (it has on C and H atoms), it is tremendously delocalized, and
not at all "drug-like".
Furthermore, you should think about what you are asking antechamber to do in
estimating charges. For a (nearly) infinite graphene sheet, the charge on
carbon would have to be zero. The charges near the edges (near hydrogens)
might be slightly different, but these would have to be fit by some novel
procedure: the "usual" methods, like RESP charges, are not designed for this
type of system. You might try some literature searches for what others have
done.
...good luck....dac
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Received on Mon Jun 17 2013 - 18:00:03 PDT
