Dear Sir
I have ligand molecule for which I am required to calculate charge and spin
multiplicity. As I am trying to run antechamber its showing error.
antechamber -i DRG_h.pdb -fi pdb -o DRG.mol2 -fo mol2 -c bcc -s 2
Here is my ligand molecule
HETATM 7193 C1 DRG 1 27.871 -19.015 31.805 1.00 0.00
C
HETATM 7194 C2 DRG 1 29.053 -18.343 31.453 1.00 0.00
C
HETATM 7195 C3 DRG 1 30.144 -19.040 30.907 1.00 0.00
C
HETATM 7196 C4 DRG 1 30.063 -20.436 30.758 1.00 0.00
C
HETATM 7197 C5 DRG 1 28.890 -21.111 31.139 1.00 0.00
C
HETATM 7198 C6 DRG 1 27.771 -20.406 31.627 1.00 0.00
C
HETATM 7199 C7 DRG 1 26.493 -21.057 31.924 1.00 0.00
C
HETATM 7200 C8 DRG 1 26.209 -22.370 31.830 1.00 0.00
C
HETATM 7201 C9 DRG 1 24.869 -22.904 32.122 1.00 0.00
C
HETATM 7202 O1 DRG 1 24.672 -24.112 32.230 1.00 0.00
O
HETATM 7203 C10 DRG 1 23.702 -21.946 32.378 1.00 0.00
C
HETATM 7204 O2 DRG 1 23.292 -21.275 31.189 1.00 0.00
O
HETATM 7205 C11 DRG 1 22.363 -20.196 31.378 1.00 0.00
C
HETATM 7206 C12 DRG 1 21.470 -20.267 32.639 1.00 0.00
C
HETATM 7207 C13 DRG 1 20.416 -19.133 32.699 1.00 0.00
C
HETATM 7208 C14 DRG 1 21.123 -17.760 32.578 1.00 0.00
C
HETATM 7209 C15 DRG 1 22.060 -17.642 31.357 1.00 0.00
C
HETATM 7210 C16 DRG 1 23.055 -18.818 31.223 1.00 0.00
C
HETATM 7211 O3 DRG 1 24.016 -18.604 32.230 1.00 0.00
O
HETATM 7212 O4 DRG 1 21.272 -17.543 30.196 1.00 0.00
O
HETATM 7213 C17 DRG 1 19.663 -19.144 34.055 1.00 0.00
C
HETATM 7214 O5 DRG 1 20.271 -19.544 35.077 1.00 0.00
O1-
HETATM 7215 O6 DRG 1 18.479 -18.741 34.060 1.00 0.00
O1-
HETATM 7216 O7 DRG 1 19.532 -19.253 31.571 1.00 0.00
O
HETATM 7217 C18 DRG 1 18.594 -20.337 31.543 1.00 0.00
C
HETATM 7218 C19 DRG 1 18.489 -20.927 30.130 1.00 0.00
C
HETATM 7219 O8 DRG 1 17.817 -21.943 29.962 1.00 0.00
O
HETATM 7220 C20 DRG 1 19.234 -20.278 29.040 1.00 0.00
C
HETATM 7221 C21 DRG 1 19.402 -20.831 27.824 1.00 0.00
C
HETATM 7222 C22 DRG 1 20.242 -20.225 26.777 1.00 0.00
C
HETATM 7223 C23 DRG 1 21.281 -19.325 27.114 1.00 0.00
C
HETATM 7224 C24 DRG 1 22.079 -18.744 26.118 1.00 0.00
C
HETATM 7225 C25 DRG 1 21.852 -19.063 24.770 1.00 0.00
C
HETATM 7226 C26 DRG 1 20.803 -19.939 24.409 1.00 0.00
C
HETATM 7227 C27 DRG 1 19.999 -20.513 25.416 1.00 0.00
C
HETATM 7228 O9 DRG 1 20.569 -20.244 23.095 1.00 0.00
O
HETATM 7229 O10 DRG 1 22.671 -18.521 23.830 1.00 0.00
O
HETATM 7230 O11 DRG 1 31.100 -21.143 30.231 1.00 0.00
O
HETATM 7231 O12 DRG 1 31.244 -18.343 30.503 1.00 0.00
O
HETATM 0 HC52 DRG 1 29.257 -22.081 31.505 1.00 0.00
H new HETATM 0 H10C DRG 1 24.133 -21.599 33.329 1.00 0.00
H new
HETATM 0 HC8 DRG 1 27.004 -23.066 31.525 1.00 0.00
H new
TER 7232 DRG 1
Here is the error detail
Total number of electrons: 261; net charge: 0
INFO: Number of electrons is odd: 261
Please check the total charge (-nc flag) and spin multiplicity (-m
flag)
Error: cannot run "/home/sabnam/amber12/bin/sqm -O -i sqm.in -o sqm.out" of
bcc() in charge.c properly, exit
I request to kindly guide me in calculating the charge and spin
multiplicity and debuging the error associated with antechamber.
Regards
Arunima
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Received on Tue Mar 04 2014 - 03:30:02 PST
