<DE_fad.pdb>_______________________________________________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
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