Hi, I am attempting to run DockPrep on NQO2 which contains an FAD cofactor. Everything works until it attempts to add charges to FAD at which point it returns an error message. If I delete FAD it will return the same error message for the Zn ion. It seems to be unable to add charges for any non-amino acid molecules. I am running the latest stable build of Chimera. Interestingly, I know Chimera used to be able to calculate these charges with an old version I had but seems no longer able. Below is the reply log. Thank you.

#0, chain A: nrh dehydrogenase [quinone] 2

#0, chain B: nrh dehydrogenase [quinone] 2

No incomplete side chains

Terminii for WT_noH.pdb (#0) chain A determined from SEQRES records

Terminii for WT_noH.pdb (#0) chain B determined from SEQRES records

Chain-initial residues that are actual N terminii: ALA 1.A, ALA 1.B

Chain-initial residues that are not actual N terminii: 

Chain-final residues that are actual C terminii: GLN 230.A, GLN 230.B

Chain-final residues that are not actual C terminii: 

482 hydrogen bonds

Hydrogens added

Charge model: AMBER ff99SB

Assigning partial charges to residue ZN (net charge +2) with am1-bcc method

Assigning partial charges to residue FAD (net charge +0) with am1-bcc method

Running ANTECHAMBER command: C:/Program Files/Chimera 1.6.2/bin/amber11/bin\antechamber -ek qm_theory='AM1', -i c:\docume~1\dylan_~1\locals~1\temp\tmpy6za6o\ante.in.mol2 -fi mol2 -o c:\docume~1\dylan_~1\locals~1\temp\tmpy6za6o\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2

(FAD) 

(FAD) 

(FAD) Total number of electrons: 407; net charge: 0

(FAD) INFO: Number of electrons is odd: 407

(FAD)       Please check the total charge (-nc flag) and spin multiplicity (-m flag)

(FAD) 

(FAD) Running: "C:/Program Files/Chimera 1.6.2/bin/amber11/bin/sqm" -O -i sqm.in -o sqm.out

(FAD) Error: cannot run ""C:/Program Files/Chimera 1.6.2/bin/amber11/bin/sqm" -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit

(FAD) Running: "C:/Program Files/Chimera 1.6.2/bin/amber11/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(FAD) 

(FAD) Running: "C:/Program Files/Chimera 1.6.2/bin/amber11/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Failure running ANTECHAMBER for residue FAD

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