---------- Forwarded message ---------
From: Todd Minehardt <todd.minehardt.gmail.com>
Date: Fri, Dec 1, 2023 at 4:45 PM
Subject: Re: [AMBER] antechamber error-- QMMM: System specified with odd
number of electrons
To: Yang, Li-Yen <zoeyxyang.gatech.edu>
Zoey,
I used Chimerax and the Tools -> Structure Editing -> Add Hydrogens option,
which added the one missing hydrogen to O9 automagically. You can certainly
do so with other tools such as pymol (but I recommend Chimerax, for what
that's worth).
I've attached the PDB generated by that - I do encourage you to go through
the exercise yourself, it is a necessary thing to know how to do - and have
run:
antechamber -i ligand_with_added_h.pdb -fi pdb -o ligand_with_added_h.mol2
-fo mol2 -c bcc -nc 0 -j 5
which is presently churning away and shows total # of electrons as 410.
Cheers,
Todd
On Fri, Dec 1, 2023 at 12:47 PM Yang, Li-Yen <zoeyxyang.gatech.edu> wrote:
> Hi Todd,
>
>
>
> Thank you so much for the response.
>
> It turns out that when I used the reduce command to reduce my ligand, it
> somehow didn’t protonate O9. (But other O works fine)
>
> Do you know how I can add a hydrogen to O9?
>
>
>
> Best,
>
> Zoey
>
>
>
> *From: *Todd Minehardt <todd.minehardt.gmail.com>
> *Date: *Thursday, November 30, 2023 at 1:17 PM
> *To: *Yang, Li-Yen <zoeyxyang.gatech.edu>, AMBER Mailing List <
> amber.ambermd.org>
> *Subject: *Re: [AMBER] antechamber error-- QMMM: System specified with
> odd number of electrons
>
> 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 Fri Dec 01 2023 - 15:30:02 PST
