On Wed, Feb 15, 2017, Aseel Bala wrote:
>
> I am trying to create an acetic acid molecule with xleap and generate a pdb
> and mol2 file. I am able to create the molecule in xleap. However, I am not
> able to add the double bond between the C and O.
The error you see has nothing to do with creating or not creating a double
bond. In fact, PDB files have no notion of bonds or bond orders, and
antechamber doesn't expect to find any such information in the PDB file.
Rather, your problem is that the z-coordinates of all atoms are zero: you
have a planar molecule(!), whereas antechamnber expects (and requires) a
reasonable input configuration.
ATOM 1 C1 aaa 1 12.735 -2.914 0.000 1.00 0.00
> ATOM 2 C2 aaa 1 11.238 -3.020 0.000 1.00 0.00
> ATOM 3 H4 aaa 1 12.805 -3.912 0.000 1.00 0.00
> ATOM 4 H5 aaa 1 13.590 -3.432 0.000 1.00 0.00
> ATOM 5 H6 aaa 1 13.253 -2.059 0.000 1.00 0.00
> ATOM 6 O7 aaa 1 11.776 -4.420 0.000 1.00 0.00
> ATOM 7 O8 aaa 1 10.057 -3.945 0.000 1.00 0.00
> ATOM 8 H9 aaa 1 9.213 -3.408 0.000 1.00 0.00
> TER
> END
>
It's not clear how you created these coordinates, but if you view your pdb
file in a molecular viewer, you will immediately see the problem. You need
to create a good geometry: in xleap, consider selecting all atoms and choosing
the "relax selection" option in the menu.
...good luck....dac
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Received on Wed Feb 15 2017 - 19:00:02 PST
