Li-Yen,
I downloaded your file and looked at it - on C27, you have 4 atoms
attached: C26, C34, H27, and O9.
Assuming that C27 is sp3 hybridized, your problem is H27 and O9, as you
either need to protonate O9 or remove H27 for a neutral charge.
Antechamber will run on your system with -nc either as 1 or -1, but your
system does have an extra electron floating around.
Cheers,
Todd
On Thu, Nov 30, 2023 at 11:02 AM Yang, Li-Yen via AMBER <amber.ambermd.org>
wrote:
> Hello,
>
> I am trying to use antechamber to create a mol2 file for my ligand.
>
> When I run the command: antechamber -i ligand_h.pdb -fi pdb -o
> ligand.mol2 -fo mol2 -c bcc -s 2 -nc 0 ,there is an error in my sqm.out
> file:
> QMMM: System specified with odd number of electrons ( 305)
> QMMM: but odd spin ( 1). You most likely have the charge of
> QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
> calculation.
>
> 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.
>
> I’m attaching my ligand_h.pdb file.
>
> Any suggestions are greatly appreciated!
>
> Best,
> Zoey
>
>
>
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Received on Thu Nov 30 2023 - 10:30:03 PST
