On Fri, Dec 08, 2023, Yang, Li-Yen via AMBER wrote:
>antechamber -i lipid_dipal_h.pdb -fi pdb -o lipid_dipal .mol2 -fo mol2 -c bcc -s 2 -nc 0
>
>sqm.out gives me a similar error:
>QMMM: System specified with odd number of electrons ( 453)
Looks to me like you input molecule should have a -1 charge because of the
phospho-diester group. But you have told antechamber that the net charge
(-nc) is zero, which implied an odd number of electrons.
>However, I’m pretty sure the charge of this ligand is 0, and I’ve
>verified that using the “charge” command in tleap.
It's hard to understand how tleap could know about the charge of your unit
if antechamber failed to create the proper library files.
...good luck...dac
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Received on Fri Dec 08 2023 - 15:30:02 PST
