Quoting Bill Ross <ross.cgl.ucsf.EDU>:
>> 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
>
Oh, I just forgot to include the error messaegs.
---------------------------------------------------
Could not find angle parameter: ce - ce - cg
Could not find angle parameter: cf - cf - ch
Could not find angle parameter: ch - cf - cf
Could not find angle parameter: cg - ce - ce
Could not find angle parameter: ce - ce - cg
Could not find angle parameter: cf - cf - ch
Could not find angle parameter: ch - cf - cf
Could not find angle parameter: cg - ce - ce
** No torsion terms for ce-ce-cg-ch
** No torsion terms for cf-cf-ch-cg
** No torsion terms for ch-cg-ce-ce
** No torsion terms for cg-ch-cf-cf
** No torsion terms for ce-ce-cg-ch
** No torsion terms for cf-cf-ch-cg
** No torsion terms for ch-cg-ce-ce
** No torsion terms for cg-ch-cf-cf
---------------------------------------------
I guess this is from the additional bonds between residues.
Thank you.
Bongkeun Kim
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Received on Wed Oct 20 2010 - 17:00:05 PDT
