Dear all,
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:
antechamber -i graphene.pdb -fi pdb -o graphene.prepin -fo prepi -c bcc -j
4 -at gaff
I received a huge amount of warnings from Antechamber about exceeding 10
residues, a final warning about reallocating memory due to exceeding
MAXBOND, and then the program appeared to freeze. I can't tell if it's
still calculating slowly or simply stuck in a loop.
Is the procedure I'm following correct for defining a graphene molecule?
Is the format of the PDB file, attached, correct? I wasn't able to find
much information about the setup online, other than that it has previously
been done. Any help would be greatly appreciated.
Thank you,
Dan
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Received on Mon Jun 17 2013 - 12:00:02 PDT
