The problem isn't that atom it's S2 which has a lower case s as the atomic
symbol. This should work.
@<TRIPOS>MOLECULE
56
56 57 1 0 0
SMALL
No Charge or Current Charge
@<TRIPOS>ATOM
1 O1 185.3370 -1.2940 41.4720 O.2 1 MOL -0.561400
2 S1 185.7170 -1.1200 40.1020 S.3 1 MOL 1.168300
3 O2 186.5760 -0.0520 39.6890 O.2 1 MOL -0.561400
4 C7 184.2740 -1.0090 39.1500 C.3 1 MOL -0.519100
5 H6 183.7180 -1.9350 39.2880 H 1 MOL 0.174600
6 H7 183.7170 -0.1510 39.5210 H 1 MOL 0.174600
7 H8 184.5630 -0.8570 38.1080 H 1 MOL 0.174600
8 N1 186.2420 -2.5640 39.4880 N.3 1 MOL -0.663100
9 H5 185.7910 -2.5910 38.5910 H 1 MOL 0.342600
10 C5 187.5810 -2.6860 39.3790 C.ar 1 MOL 0.400800
11 C6 188.3570 -2.9100 40.5080 C.ar 1 MOL -0.263400
12 C1 189.7410 -3.0320 40.3880 C.ar 1 MOL -0.211300
13 H1 190.3340 -3.2080 41.2810 H 1 MOL 0.169200
14 H4 187.8790 -2.9910 41.4810 H 1 MOL 0.188700
15 C4 188.1790 -2.5970 38.1250 C.ar 1 MOL -0.263400
16 H3 187.5740 -2.4410 37.2360 H 1 MOL 0.188700
17 C3 189.5670 -2.6730 38.0080 C.ar 1 MOL -0.211300
18 H2 190.0410 -2.5530 37.0340 H 1 MOL 0.169200
19 C2 190.3550 -2.8940 39.1370 C.ar 1 MOL 0.066300
20 C8 191.8610 -2.9700 38.9500 C.3 1 MOL -0.097700
21 H9 192.0950 -3.8820 38.3980 H 1 MOL 0.062100
22 H10 192.1620 -2.1510 38.2990 H 1 MOL 0.062100
23 C9 192.7200 -2.9500 40.2260 C.3 1 MOL 0.137500
24 H11 192.4490 -3.8260 40.8230 H 1 MOL 0.020500
25 H12 193.7680 -3.0340 39.9420 H 1 MOL 0.020500
26 N2 192.5120 -1.7100 41.0170 N.3 1 MOL -0.391700
27 C10 192.8750 -1.8910 42.4390 C.3 1 MOL -0.010500
28 H13 192.5690 -1.0190 43.0170 H 1 MOL 0.053900
29 H14 192.3570 -2.7590 42.8510 H 1 MOL 0.053900
30 H15 193.9520 -2.0370 42.5450 H 1 MOL 0.053900
31 C11 193.1530 -0.5120 40.4040 C.3 1 MOL -0.261800
32 H16 194.2330 -0.5440 40.5530 H 1 MOL 0.126000
33 H17 192.9670 -0.5070 39.3340 H 1 MOL 0.126000
34 C12 192.6130 0.8290 40.9290 C.3 1 MOL 0.600200
35 H18 192.6080 0.8470 42.0180 H 1 MOL -0.077700
36 H19 191.6020 1.0090 40.5550 H 1 MOL -0.077700
37 O3 193.5060 1.8730 40.4990 O.3 1 MOL -0.520900
38 C16 193.1590 2.6170 39.4070 C.ar 1 MOL 0.466000
39 C17 193.2050 2.0860 38.1230 C.ar 1 MOL -0.351200
40 C18 192.8510 2.8760 37.0240 C.ar 1 MOL -0.194300
41 H23 192.9040 2.4540 36.0250 H 1 MOL 0.190200
42 H22 193.5390 1.0680 37.9730 H 1 MOL 0.185000
43 C15 192.7790 3.9400 39.5900 C.ar 1 MOL -0.351200
44 H21 192.7650 4.3400 40.5950 H 1 MOL 0.185000
45 C14 192.4310 4.7360 38.4930 C.ar 1 MOL -0.194300
46 H20 192.1510 5.7760 38.6460 H 1 MOL 0.190200
47 C13 192.4470 4.2020 37.2040 C.ar 1 MOL 0.318600
48 N3 192.1310 5.0130 36.1600 N.3 1 MOL -0.708800
49 H24 191.7160 5.8940 36.4060 H 1 MOL 0.373500
50 S2 191.1040 4.5350 34.9520 S.3 1 MOL 1.204100
51 O5 190.4610 3.2930 35.2520 O.2 1 MOL -0.577800
52 C19 192.2620 4.2850 33.6910 C.3 1 MOL -0.528100
53 H25 191.7040 4.0120 32.7980 H 1 MOL 0.176400
54 H26 192.9290 3.4880 34.0090 H 1 MOL 0.176400
55 H27 192.7940 5.2260 33.5650 H 1 MOL 0.176400
56 O4 190.3350 5.6910 34.6150 O.2 1 MOL -0.577800
@<TRIPOS>BOND
1 52 53 1
2 52 54 1
3 52 55 1
4 50 51 1
5 50 52 1
6 50 56 1
7 48 49 1
8 48 50 1
9 47 48 1
10 45 46 1
11 45 47 ar
12 43 44 1
13 43 45 ar
14 40 41 1
15 40 47 ar
16 39 40 ar
17 39 42 1
18 38 39 ar
19 38 43 ar
20 37 38 1
21 34 35 1
22 34 36 1
23 34 37 1
24 31 32 1
25 31 33 1
26 31 34 1
27 27 28 1
28 27 29 1
29 27 30 1
30 26 27 1
31 26 31 1
32 23 24 1
33 23 25 1
34 23 26 1
35 20 21 1
36 20 22 1
37 20 23 1
38 19 20 1
39 17 18 1
40 17 19 ar
41 15 16 1
42 15 17 ar
43 12 13 1
44 12 19 ar
45 11 12 ar
46 11 14 1
47 10 11 ar
48 10 15 ar
49 8 9 1
50 8 10 1
51 4 5 1
52 4 6 1
53 4 7 1
54 2 3 1
55 2 4 1
56 2 8 1
57 1 2 1
@<TRIPOS>SUBSTRUCTURE
1 MOL 1 TEMP 0 **** **** 0 ROOT
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
| SM2 5NG
T 020 8722 4033 | E [email protected] | W www.icr.ac.uk | Twitter
@ICRnews
________________________________________
From: Wong, Sergio E. [[email protected]]
Sent: 04 August 2014 21:37
To: [email protected]
Subject: [Rdkit-discuss] can not read in sulfur in mol2 file
Hi;
I am using the RDkit python libraries to read in a mol2 file and create a
molecule. The code reads:
mol = Chem.MolFromMol2File("FILENAME")
I get the following error message:
****
Post-condition Violation
Element 's' not found
Violation occurred on line 91 in file
/home/wong105/usr/RDKit/Code/GraphMol/PeriodicTable.h
Failed Expression: anum>-1
****
Any suggestions? The mol2 file is shown below. The sulfur atom is S1 (number
2) in the file.
Thanks;
-Sergio
@<TRIPOS>MOLECULE
56
56 57 1 0 0
SMALL
No Charge or Current Charge
@<TRIPOS>ATOM
1 O1 185.3370 -1.2940 41.4720 O.2 1 MOL -0.561400
2 S1 185.7170 -1.1200 40.1020 S.3 1 MOL 1.168300
3 O2 186.5760 -0.0520 39.6890 O.2 1 MOL -0.561400
4 C7 184.2740 -1.0090 39.1500 C.3 1 MOL -0.519100
5 H6 183.7180 -1.9350 39.2880 H 1 MOL 0.174600
6 H7 183.7170 -0.1510 39.5210 H 1 MOL 0.174600
7 H8 184.5630 -0.8570 38.1080 H 1 MOL 0.174600
8 N1 186.2420 -2.5640 39.4880 N.3 1 MOL -0.663100
9 H5 185.7910 -2.5910 38.5910 H 1 MOL 0.342600
10 C5 187.5810 -2.6860 39.3790 C.ar 1 MOL 0.400800
11 C6 188.3570 -2.9100 40.5080 C.ar 1 MOL -0.263400
12 C1 189.7410 -3.0320 40.3880 C.ar 1 MOL -0.211300
13 H1 190.3340 -3.2080 41.2810 H 1 MOL 0.169200
14 H4 187.8790 -2.9910 41.4810 H 1 MOL 0.188700
15 C4 188.1790 -2.5970 38.1250 C.ar 1 MOL -0.263400
16 H3 187.5740 -2.4410 37.2360 H 1 MOL 0.188700
17 C3 189.5670 -2.6730 38.0080 C.ar 1 MOL -0.211300
18 H2 190.0410 -2.5530 37.0340 H 1 MOL 0.169200
19 C2 190.3550 -2.8940 39.1370 C.ar 1 MOL 0.066300
20 C8 191.8610 -2.9700 38.9500 C.3 1 MOL -0.097700
21 H9 192.0950 -3.8820 38.3980 H 1 MOL 0.062100
22 H10 192.1620 -2.1510 38.2990 H 1 MOL 0.062100
23 C9 192.7200 -2.9500 40.2260 C.3 1 MOL 0.137500
24 H11 192.4490 -3.8260 40.8230 H 1 MOL 0.020500
25 H12 193.7680 -3.0340 39.9420 H 1 MOL 0.020500
26 N2 192.5120 -1.7100 41.0170 N.3 1 MOL -0.391700
27 C10 192.8750 -1.8910 42.4390 C.3 1 MOL -0.010500
28 H13 192.5690 -1.0190 43.0170 H 1 MOL 0.053900
29 H14 192.3570 -2.7590 42.8510 H 1 MOL 0.053900
30 H15 193.9520 -2.0370 42.5450 H 1 MOL 0.053900
31 C11 193.1530 -0.5120 40.4040 C.3 1 MOL -0.261800
32 H16 194.2330 -0.5440 40.5530 H 1 MOL 0.126000
33 H17 192.9670 -0.5070 39.3340 H 1 MOL 0.126000
34 C12 192.6130 0.8290 40.9290 C.3 1 MOL 0.600200
35 H18 192.6080 0.8470 42.0180 H 1 MOL -0.077700
36 H19 191.6020 1.0090 40.5550 H 1 MOL -0.077700
37 O3 193.5060 1.8730 40.4990 O.3 1 MOL -0.520900
38 C16 193.1590 2.6170 39.4070 C.ar 1 MOL 0.466000
39 C17 193.2050 2.0860 38.1230 C.ar 1 MOL -0.351200
40 C18 192.8510 2.8760 37.0240 C.ar 1 MOL -0.194300
41 H23 192.9040 2.4540 36.0250 H 1 MOL 0.190200
42 H22 193.5390 1.0680 37.9730 H 1 MOL 0.185000
43 C15 192.7790 3.9400 39.5900 C.ar 1 MOL -0.351200
44 H21 192.7650 4.3400 40.5950 H 1 MOL 0.185000
45 C14 192.4310 4.7360 38.4930 C.ar 1 MOL -0.194300
46 H20 192.1510 5.7760 38.6460 H 1 MOL 0.190200
47 C13 192.4470 4.2020 37.2040 C.ar 1 MOL 0.318600
48 N3 192.1310 5.0130 36.1600 N.3 1 MOL -0.708800
49 H24 191.7160 5.8940 36.4060 H 1 MOL 0.373500
50 S2 191.1040 4.5350 34.9520 s.3 1 MOL 1.204100
51 O5 190.4610 3.2930 35.2520 O.2 1 MOL -0.577800
52 C19 192.2620 4.2850 33.6910 C.3 1 MOL -0.528100
53 H25 191.7040 4.0120 32.7980 H 1 MOL 0.176400
54 H26 192.9290 3.4880 34.0090 H 1 MOL 0.176400
55 H27 192.7940 5.2260 33.5650 H 1 MOL 0.176400
56 O4 190.3350 5.6910 34.6150 O.2 1 MOL -0.577800
@<TRIPOS>BOND
1 52 53 1
2 52 54 1
3 52 55 1
4 50 51 1
5 50 52 1
6 50 56 1
7 48 49 1
8 48 50 1
9 47 48 1
10 45 46 1
11 45 47 ar
12 43 44 1
13 43 45 ar
14 40 41 1
15 40 47 ar
16 39 40 ar
17 39 42 1
18 38 39 ar
19 38 43 ar
20 37 38 1
21 34 35 1
22 34 36 1
23 34 37 1
24 31 32 1
25 31 33 1
26 31 34 1
27 27 28 1
28 27 29 1
29 27 30 1
30 26 27 1
31 26 31 1
32 23 24 1
33 23 25 1
34 23 26 1
35 20 21 1
36 20 22 1
37 20 23 1
38 19 20 1
39 17 18 1
40 17 19 ar
41 15 16 1
42 15 17 ar
43 12 13 1
44 12 19 ar
45 11 12 ar
46 11 14 1
47 10 11 ar
48 10 15 ar
49 8 9 1
50 8 10 1
51 4 5 1
52 4 6 1
53 4 7 1
54 2 3 1
55 2 4 1
56 2 8 1
57 1 2 1
@<TRIPOS>SUBSTRUCTURE
1 MOL 1 TEMP 0 **** **** 0 ROOT
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