Dear David,
Please find attached the input pdb file for the ligand. The charge is -1, I
used -nc flag to specify the charge of the system. Is that correct? By the
way, the ligand already has hydrogens before using antechamber.
antechamber -i 6058_rep0_pose1.pdb -fi pdb -nc -1 -o 6058_rep0_pose1.mol2
-fo mol2 -c bcc
I check the sqm.out file, the calculation is completed.
Best regards,
Rui
On Thu, Nov 21, 2019 at 6:34 AM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Nov 20, 2019, Rui Chen wrote:
> >
> >QMMM: System specified with odd number of electrons ( 141)
> >QMMM: but odd spin ( 1). You most likely have the charge of
> >QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
> >calculation.
>
> This shows that something is wrong with your input files; are all the
> hydrogens present? Have you specified the charge of the molecule (if it
> is not zero)?
>
> >Instead of using bcc charge method, I used gas charge method,
>
> Gasteiger charges are not likely to be very accurate. Plus, if you
> don't have the proper net charge on the molecule, any charge method will
> be dramatically wrong. Bottom line: you need to fix the problem
> identified above before proceeding.
>
> ...good luck...dac
>
>
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Received on Thu Nov 21 2019 - 09:00:02 PST
