Hi,
I am trying to run antechamber using ambertools 13 for this molecule:
ATOM 1 O 1 -9.081 -2.322 -3.462
ATOM 2 C 1 -8.756 -3.677 -3.819
ATOM 3 C 1 -7.666 -4.201 -2.904
ATOM 4 O 1 -6.413 -3.571 -3.239
ATOM 5 C 1 -7.920 -3.956 -1.399
ATOM 6 O 1 -7.696 -5.223 -0.723
ATOM 7 C 1 -6.909 -2.874 -1.042
ATOM 8 C 1 -5.771 -3.097 -2.040
ATOM 9 N 1 -5.000 -1.912 -2.355
ATOM 10 C 1 -5.455 -0.694 -2.836
ATOM 11 N 1 -4.495 0.181 -3.049
ATOM 12 C 1 -3.340 -0.494 -2.690
ATOM 13 C 1 -1.977 -0.117 -2.699
ATOM 14 N 1 -1.541 1.092 -3.096
ATOM 15 N 1 -1.075 -1.039 -2.279
ATOM 16 C 1 -1.497 -2.256 -1.882
ATOM 17 N 1 -2.746 -2.724 -1.848
ATOM 18 C 1 -3.622 -1.795 -2.262
ATOM 19 P 1 -7.975 -5.326 0.889
ATOM 20 O 1 -8.413 -6.749 1.185
ATOM 21 O 1 -8.912 -4.227 1.366
ATOM 22 O 1 -6.505 -5.025 1.545
ATOM 23 C 1 -5.455 -5.974 1.233
ATOM 24 C 1 -4.210 -5.630 2.023
ATOM 25 O 1 -3.704 -4.359 1.578
ATOM 26 C 1 -4.398 -5.547 3.564
ATOM 27 O 1 -3.534 -6.445 4.276
ATOM 28 C 1 -4.149 -4.066 3.869
ATOM 29 C 1 -3.249 -3.611 2.717
ATOM 30 N 1 -3.312 -2.194 2.397
ATOM 31 C 1 -2.111 -1.456 2.389
ATOM 32 O 1 -1.029 -1.944 2.713
ATOM 33 N 1 -2.258 -0.143 2.008
ATOM 34 C 1 -3.432 0.499 1.639
ATOM 35 O 1 -3.421 1.699 1.302
ATOM 36 C 1 -4.639 -0.315 1.676
ATOM 37 C 1 -5.944 0.316 1.288
ATOM 38 C 1 -4.513 -1.617 2.035
ATOM 39 H 1 -2.220 1.759 -3.436
ATOM 40 H 1 -0.528 1.282 -3.162
ATOM 41 H 1 -0.705 -2.926 -1.546
ATOM 42 H 1 -6.510 -0.529 -3.029
ATOM 43 H 1 -5.039 -3.832 -1.676
ATOM 44 H 1 -7.367 -1.894 -1.218
ATOM 45 H 1 -6.577 -2.933 -0.003
ATOM 46 H 1 -9.642 -4.329 -3.717
ATOM 47 H 1 -8.391 -3.737 -4.855
ATOM 48 H 1 -9.506 -1.908 -4.230
ATOM 49 H 1 -7.580 -5.288 -3.063
ATOM 50 H 1 -8.946 -3.630 -1.197
ATOM 51 H 1 -5.788 -6.991 1.488
ATOM 52 H 1 -5.230 -5.933 0.158
ATOM 53 H 1 -3.466 -6.420 1.814
ATOM 54 H 1 -5.408 -5.852 3.851
ATOM 55 H 1 -2.616 -6.261 4.009
ATOM 56 H 1 -5.098 -3.518 3.834
ATOM 57 H 1 -3.692 -3.923 4.855
ATOM 58 H 1 -2.183 -3.802 2.914
ATOM 59 H 1 -6.767 -0.405 1.355
ATOM 60 H 1 -5.894 0.708 0.263
ATOM 61 H 1 -6.168 1.171 1.938
ATOM 62 H 1 -5.363 -2.298 2.044
ATOM 63 H 1 -1.350 0.426 1.968
TER
using this command:
antechaber -i b.pdb -fi pdb -o b.mol2 -fo mol2 -c bcc -at amber -nc -1
and I get the following error:
Error: cannot run "/home/rodrigo/amber12/bin/sqm -O -i sqm.in -o sqm.out"
of bcc() in charge.c properly, exit
Any ideas?
Regards
Rodrigo Salazar
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Received on Tue Sep 03 2013 - 18:30:02 PDT
