Segmentation fault (core dumped) #5
Description
Hi,
I was playing around with pyDockRMSD but got a "Segmentation fault (core dumped)" error. I wonder how this could be solved. Here I have attached the two mol2 files I used. Both of them were converted from PDB files. One of PDB files was converted from an SDF file.
Here are the contents of the two mol2 files if they help:
mol_1.mol2
@<TRIPOS>MOLECULE
pdb1.pdb
23 23 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C1 13.3050 20.7000 59.4050 C.3 1 UNL1 0.1695
2 C2 12.4520 19.8420 58.4700 C.3 1 UNL1 0.0315
3 C3 12.0320 18.5340 59.1240 C.3 1 UNL1 0.0023
4 C4 11.2470 17.6310 58.1880 C.3 1 UNL1 0.0001
5 C5 12.1070 17.1040 57.0260 C.3 1 UNL1 0.0000
6 C6 14.7350 20.9920 55.3470 C.ar 1 UNL1 0.0372
7 C7 15.1480 21.1380 54.0250 C.ar 1 UNL1 0.0031
8 C8 16.3840 21.7100 53.7410 C.ar 1 UNL1 0.0002
9 C9 17.2110 22.1400 54.7700 C.ar 1 UNL1 0.0031
10 C10 16.7990 21.9980 56.0940 C.ar 1 UNL1 0.0372
11 C11 15.5620 21.4200 56.3890 C.ar 1 UNL1 0.1436
12 C12 12.7980 20.9330 61.8050 C.2 1 UNL1 0.2422
13 C13 11.7430 20.6960 64.1740 C.3 1 UNL1 0.0513
14 C14 11.8610 21.4970 62.8700 C.3 1 UNL1 0.0927
15 C15 11.1530 19.2930 64.0350 C.2 1 UNL1 0.0508
16 O1 12.9990 22.5100 57.5130 O.co2 1 UNL1 -0.7704
17 O2 14.5790 22.9640 59.4710 O.2 1 UNL1 -0.2908
18 O3 15.1750 21.2220 57.7500 O.3 1 UNL1 -0.4489
19 O4 13.7620 20.2300 62.1210 O.2 1 UNL1 -0.2733
20 O5 11.9380 18.3450 64.0180 O.co2 1 UNL1 -0.5492
21 O6 9.9630 19.1340 64.3110 O.co2 1 UNL1 -0.5492
22 N1 12.4830 21.1820 60.5180 N.am 1 UNL1 -0.1974
23 P1 13.9840 22.0210 58.4990 P.3 1 UNL1 0.2141
@<TRIPOS>UNITY_ATOM_ATTR
16 1
charge -1
21 1
charge -1
@<TRIPOS>BOND
1 1 2 1
2 1 22 1
3 1 23 1
4 2 3 1
5 3 4 1
6 4 5 1
7 6 7 ar
8 6 11 ar
9 7 8 ar
10 8 9 ar
11 9 10 ar
12 10 11 ar
13 11 18 1
14 12 14 1
15 12 19 2
16 12 22 am
17 13 14 1
18 13 15 1
19 15 20 ar
20 15 21 ar
21 16 23 1
22 17 23 2
23 18 23 1
mol_2.mol2
@<TRIPOS>MOLECULE
pdb2.pdb
23 23 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C38 -8.9400 10.6200 -15.8520 C.3 1 LIG1 0.0000
2 C41 -8.8870 10.1720 -17.2720 C.3 1 LIG1 0.0001
3 C42 -7.9110 10.9980 -18.1080 C.3 1 LIG1 0.0025
4 C43 -6.5510 10.8840 -17.6050 C.3 1 LIG1 0.0355
5 C44 -5.5230 11.7900 -18.2370 C.3 1 LIG1 0.2125
6 N37 -5.3580 11.5680 -19.6350 N.am 1 LIG1 -0.1934
7 C30 -5.2910 12.5680 -20.5030 C.2 1 LIG1 0.2425
8 O24 -5.4110 13.7320 -20.1400 O.2 1 LIG1 -0.2733
9 C40 -5.0680 12.1660 -21.9650 C.3 1 LIG1 0.0986
10 C39 -5.6020 13.1880 -22.9180 C.3 1 LIG1 0.1237
11 C29 -4.6320 14.3120 -23.0830 C.2 1 LIG1 0.3654
12 O23 -3.4170 14.1500 -22.8690 O.co2 1 LIG1 -0.2456
13 O26 -5.0700 15.3940 -23.4770 O.co2 1 LIG1 -0.2456
14 P45 -4.0050 11.4520 -17.4790 P.3 1 LIG1 0.4369
15 O25 -3.7640 9.9630 -17.4970 O.2 1 LIG1 -0.2393
16 O27 -2.9380 12.1960 -18.1660 O.3 1 LIG1 -0.1284
17 O28 -4.2910 12.0170 -16.0220 O.3 1 LIG1 -0.4198
18 C36 -3.5410 11.5700 -14.9110 C.ar 1 LIG1 0.1468
19 C34 -3.9700 10.4500 -14.1970 C.ar 1 LIG1 0.0374
20 C32 -3.2730 10.0100 -13.0970 C.ar 1 LIG1 0.0031
21 C31 -2.1280 10.7200 -12.6740 C.ar 1 LIG1 0.0002
22 C33 -1.7230 11.8440 -13.3820 C.ar 1 LIG1 0.0031
23 C35 -2.4350 12.2760 -14.4750 C.ar 1 LIG1 0.0374
@<TRIPOS>BOND
1 1 2 1
2 2 3 1
3 3 4 1
4 4 5 1
5 5 6 1
6 6 7 am
7 7 8 2
8 7 9 1
9 9 10 1
10 10 11 1
11 11 12 ar
12 11 13 ar
13 5 14 1
14 14 15 2
15 14 16 1
16 14 17 1
17 17 18 1
18 18 19 ar
19 19 20 ar
20 20 21 ar
21 21 22 ar
22 22 23 ar
23 18 23 ar
Thanks so much for your help!