Hello,
I am trying to use antechamber to create a mol2 file for my ligand.
I first used the reduce command to reduce my ligand and produced a file lipid_dipal_h.pdb.
When I ran:
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)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
I checked lipid_dipal_h.pdb in Pymol, but I can’t find anything wrong with it.
It seems like all the hydrogens are added properly. I couldn’t figure out why this is not working for antechamber.
I’m attaching the file lipid_dipal_h.pdb.
Does anyone know how to solve this problem?
I tried looking up similar errors online, and I saw that it might be resulting from the incorrect specification of the charge (-nc).
However, I’m pretty sure the charge of this ligand is 0, and I’ve verified that using the “charge” command in tleap.
Any suggestions are greatly appreciated!
Best,
Zoey
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Received on Fri Dec 08 2023 - 13:00:03 PST
