[Chimera-users] Error in generating sqm for FAD

[Isha]

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/binantechamber -ek qm_theory='AM1', -i
c:usersamehtaappdatalocaltemptmpjjpoaqante.in.mol2 -fi mol2 -o
c:usersamehtaappdatalocaltemptmpjjpoaqante.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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