> I just went back to the residue level.
>
> I made a small graphite with 4 ring including 16 atoms(4-1.pdb)
> And I was able to have prepi and frcmod file after
> -----------
> antechamber -fi mol2 -fo prepi -i 4c.mol2 -o 4c.prepi -j both -c bcc -rn GRP
> parmchk -i 4c.prepi -o 4c.frcmod -f prepc
> ------------
One thing just occurred to me: I see in your prepi that your
carbons have different types. E.g.
> 4 C cg M 3 2 1 1.540 111.208 180.000 -0.100300
> 5 C1 ch M 4 3 2 1.421 30.003 177.258 0.016700
> 6 C2 cf M 5 4 3 1.421 119.918 175.254 -0.107800
> 7 C3 c1 M 6 5 4 1.421 119.973 179.997 0.288100
> 17 C13 ce M 16 15 14 1.421 119.973 -4.747 -0.107800
I expect that and presumably the charges reflect the fact that
you have parameterized your rings as a standalone molecule. I
am not sure what antechamber can do better, but it seems like
you would want more uniformity in a larger sheet. This is why
I was originally discussing the need to have edge and corner
residues distinct from the ones that would make up the body of
the sheet.
Maybe someone else can comment on this and whether antechamber is
appropriate to the task. Perhaps you could use the current prepi
and make the atom types all match the inner carbon type - my
impression is that the sheet is a hexagonal lattice with all
interior atoms topologically the same.
I'm not sure what the charges would be in such a situation - 0?
So you may be able to proceed without antechamber or other
computational parameterization approaches if you don't care
about edge effects.
> With XtalUtilities, I have a bigger graphite structure 44.pdb by
> ------------------------------------
> PropPDB -p 4-1.pdb -o 44.pdb -X 2.461 -Y 2.842 -Z 6.708 -a 90 -b 90 -g
> 90 -ix 4 -iy 4 -iz 1
> --------------------------------------------
>
> But after running leap, I got many missing parameter error than were
> not generated parmchk.
> Could you help me how to fix this problem?
Possibly this is from added bonds involving the edge types as you
stitch the residues together? It would have been good to see the
messages. In any case, if you can reasonably change all the types
to the interior one, these messages might go away.
Bill
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Received on Wed Oct 20 2010 - 17:00:04 PDT
