Dear Sir/Mam

 I used antechamber in chimera to add charges to ligand "FAD" using am-bcc, amber ffo3r.1 and +5 charge (as depicted by chimera). The procedure was Tools > structure editing > add H and then add charge. The error shown is :

Charge model: AMBER ff03.r1
Assigning partial charges to residue FAD (net charge +1) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i c:\users\amehta\appdata\local\temp\tmpjjpoaq\ante.in.mol2 -fi mol2 -o c:\users\amehta\appdata\local\temp\tmpjjpoaq\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2
(FAD)

(FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(FAD)

(FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(FAD) Total number of electrons: 412; net charge: 1

(FAD)

(FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out

(FAD) Error: cannot run ""C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit

Failure running ANTECHAMBER for residue FAD

Please help as it is very urgent. Hope for your reply. I have also attached the ligand. Please find the attachment.

With Regards,
Isha
C/O Dr. Raman Parkesh
Protein Science & Engg.
Institute of Microbial Technology
Sector 39A, Chandigarh 160036
Ext: 0172-6665489