User 0f28873a29
23-03-2009 19:32:00
We are trying to convert small molecules from SMILE to Sybyl mol2. We realize that the Sybyl atoms types are wrong in the obtained mol2.There are any options to put these atoms types correctly?
we run this option:
molconvert -Xmx512m -g -v -3:"{fine}" mol2 inmputfile.smi -o output.mol2
A wrong file is as :
@MOLECULE
23963256_pubchem
41 43
SMALL
NO_CHARGES
@ATOM
1 H1 -1.9393 3.1422 2.4307 H
2 N1 -1.9785 2.2472 2.1857 N
3 C1 -1.8991 2.1393 0.8827 C
4 O1 -1.6998 3.2109 0.3104 O
5 C2 -1.9559 0.9588 0.0355 C
6 H2 -2.5054 0.1446 0.4943 H
7 H3 -2.5205 1.2128 -0.8655 H
8 O2 -0.7265 0.5925 -0.3644 O
9 C3 -0.1571 -0.5179 -0.3388 C
10 O3 -0.6247 -1.4939 0.2376 O
11 C4 1.0791 -0.6551 -1.0745 C
12 H4 1.3457 -1.7087 -1.1924 H
13 H5 0.9186 -0.2574 -2.0817 H
14 N2 2.1615 0.0219 -0.4386 N.ar
15 N3 2.6487 1.1582 -0.8220 N.ar
16 N4 3.6483 1.4567 -0.0613 N.ar
17 C5 3.7898 0.4616 0.8281 C.ar
18 N5 2.8217 -0.4328 0.5772 N.ar
19 C6 4.7920 0.3689 1.8284 C.ar
20 C7 5.7189 1.4233 2.0237 C.ar
21 H6 5.6817 2.2683 1.4484 H
22 C8 6.7176 1.3366 3.0111 C.ar
23 H7 7.3786 2.1066 3.1395 H
24 C9 6.8095 0.1907 3.8194 C.ar
25 H8 7.5333 0.1288 4.5398 H
26 C10 5.9064 -0.8705 3.6333 C.ar
27 H9 5.9793 -1.7088 4.2146 H
28 C11 4.9059 -0.7825 2.6469 C.ar
29 H10 4.2677 -1.5741 2.5320 H
30 C12 -1.9616 1.3763 3.1911 C.ar
31 C13 -1.2462 1.8028 4.3321 C.ar
32 H11 -0.8058 2.7267 4.3529 H
33 C14 -1.1154 0.9729 5.4578 C.ar
34 H12 -0.5920 1.3001 6.2728 H
35 C15 -1.7029 -0.3023 5.4635 C.ar
36 H13 -1.5805 -0.8989 6.2886 H
37 C16 -2.4638 -0.7315 4.3546 C.ar
38 C17 -3.0287 -1.9074 4.3722 C
39 N6 -3.5151 -2.9473 4.3908 N
40 C18 -2.6160 0.1217 3.2369 C.ar
41 H14 -3.2305 -0.1659 2.4756 H
@BOND
1 1 2 1
2 2 3 1
3 3 4 2
4 3 5 1
5 5 6 1
6 5 7 1
7 5 8 1
8 8 9 1
9 9 10 2
10 9 11 1
11 11 12 1
12 11 13 1
13 11 14 1
14 14 15 ar
15 15 16 ar
16 16 17 ar
17 17 18 ar
18 14 18 ar
19 17 19 1
20 19 20 ar
21 20 21 1
22 20 22 ar
23 22 23 1
24 22 24 ar
25 24 25 1
26 24 26 ar
27 26 27 1
28 26 28 ar
29 19 28 ar
30 28 29 1
31 2 30 1
32 30 31 ar
33 31 32 1
34 31 33 ar
35 33 34 1
36 33 35 ar
37 35 36 1
38 35 37 ar
39 37 38 1
40 38 39 3
41 37 40 ar
42 30 40 ar
43 40 41 1
@SUBSTRUCTURE
1 noname 1
This type of atoms is not the atoms of sybyl format.
we run this option:
molconvert -Xmx512m -g -v -3:"{fine}" mol2 inmputfile.smi -o output.mol2
A wrong file is as :
@MOLECULE
23963256_pubchem
41 43
SMALL
NO_CHARGES
@ATOM
1 H1 -1.9393 3.1422 2.4307 H
2 N1 -1.9785 2.2472 2.1857 N
3 C1 -1.8991 2.1393 0.8827 C
4 O1 -1.6998 3.2109 0.3104 O
5 C2 -1.9559 0.9588 0.0355 C
6 H2 -2.5054 0.1446 0.4943 H
7 H3 -2.5205 1.2128 -0.8655 H
8 O2 -0.7265 0.5925 -0.3644 O
9 C3 -0.1571 -0.5179 -0.3388 C
10 O3 -0.6247 -1.4939 0.2376 O
11 C4 1.0791 -0.6551 -1.0745 C
12 H4 1.3457 -1.7087 -1.1924 H
13 H5 0.9186 -0.2574 -2.0817 H
14 N2 2.1615 0.0219 -0.4386 N.ar
15 N3 2.6487 1.1582 -0.8220 N.ar
16 N4 3.6483 1.4567 -0.0613 N.ar
17 C5 3.7898 0.4616 0.8281 C.ar
18 N5 2.8217 -0.4328 0.5772 N.ar
19 C6 4.7920 0.3689 1.8284 C.ar
20 C7 5.7189 1.4233 2.0237 C.ar
21 H6 5.6817 2.2683 1.4484 H
22 C8 6.7176 1.3366 3.0111 C.ar
23 H7 7.3786 2.1066 3.1395 H
24 C9 6.8095 0.1907 3.8194 C.ar
25 H8 7.5333 0.1288 4.5398 H
26 C10 5.9064 -0.8705 3.6333 C.ar
27 H9 5.9793 -1.7088 4.2146 H
28 C11 4.9059 -0.7825 2.6469 C.ar
29 H10 4.2677 -1.5741 2.5320 H
30 C12 -1.9616 1.3763 3.1911 C.ar
31 C13 -1.2462 1.8028 4.3321 C.ar
32 H11 -0.8058 2.7267 4.3529 H
33 C14 -1.1154 0.9729 5.4578 C.ar
34 H12 -0.5920 1.3001 6.2728 H
35 C15 -1.7029 -0.3023 5.4635 C.ar
36 H13 -1.5805 -0.8989 6.2886 H
37 C16 -2.4638 -0.7315 4.3546 C.ar
38 C17 -3.0287 -1.9074 4.3722 C
39 N6 -3.5151 -2.9473 4.3908 N
40 C18 -2.6160 0.1217 3.2369 C.ar
41 H14 -3.2305 -0.1659 2.4756 H
@BOND
1 1 2 1
2 2 3 1
3 3 4 2
4 3 5 1
5 5 6 1
6 5 7 1
7 5 8 1
8 8 9 1
9 9 10 2
10 9 11 1
11 11 12 1
12 11 13 1
13 11 14 1
14 14 15 ar
15 15 16 ar
16 16 17 ar
17 17 18 ar
18 14 18 ar
19 17 19 1
20 19 20 ar
21 20 21 1
22 20 22 ar
23 22 23 1
24 22 24 ar
25 24 25 1
26 24 26 ar
27 26 27 1
28 26 28 ar
29 19 28 ar
30 28 29 1
31 2 30 1
32 30 31 ar
33 31 32 1
34 31 33 ar
35 33 34 1
36 33 35 ar
37 35 36 1
38 35 37 ar
39 37 38 1
40 38 39 3
41 37 40 ar
42 30 40 ar
43 40 41 1
@SUBSTRUCTURE
1 noname 1
This type of atoms is not the atoms of sybyl format.