Hello OpenBabel developers and users,
probably you could help me with a simple problem. I have two molecules
(attached) to compute all-atom RMSD between them; they are same at all
except the position in the space (docking result and a cocrystal
structure). The only problem is that they have different atom numbering,
so RMSD-computing tools using atom numbers such as VMD RMSD Calculator
plugin give unreasonable numbers (about 5 A in this case, which is
obviously wrong).
The question is: is it possible to change only atom numbering in one or
both molecules to make it the same for them, e.g. canonical? Or one of
them can be used as a template? Manual correction is hardly acceptable
because I have a series of complexes, not one. I also don't need
translation or rotation of the molecules, just compute RMSD between the
given positions.
Thanks in advance,
Dmitry Osolodkin
--
Dmitry Osolodkin
Researcher
Group of Computational Molecular Design
Department of Chemistry
Moscow State University
Moscow 119991 Russia
e-mail: dmitr...@qsar.chem.msu.ru
Phone: +7-495-9393557
Fax: +7-495-9390290
# Name: 1UV5_extract
# Creating user name: mitya
# Creation time: Wed Sep 22 16:51:03 2010
# Modifying user name: mitya
# Modification time: Wed Sep 22 16:51:03 2010
@<TRIPOS>MOLECULE
1UV5_extract
32 35 1 0 0
SMALL
NO_CHARGES
@<TRIPOS>ATOM
1 C1 -8.0310 12.6462 68.3649 C.ar 1 <1> 0.0000
2 C2 -8.3927 11.4482 69.0107 C.ar 1 <1> 0.0000
3 C3 -7.4193 10.5542 69.4706 C.ar 1 <1> 0.0000
4 C4 -6.0935 10.8813 69.2719 C.ar 1 <1> 0.0000
5 C5 -5.7481 12.0779 68.6265 C.ar 1 <1> 0.0000
6 C6 -6.6893 12.9756 68.1646 C.ar 1 <1> 0.0000
7 H1 -6.4138 13.8978 67.6674 H 1 <1> 0.0000
8 C7 -4.2761 12.1163 68.5789 C.2 1 <1> 0.0000
9 N1 -3.5529 13.0463 68.0673 N.2 1 <1> 0.0000
10 O1 -4.3967 14.0351 67.5529 O.3 1 <1> 0.0000
11 H2 -3.7575 14.6759 67.1977 H 1 <1> 0.0000
12 C8 -3.8283 10.8448 69.2498 C.2 1 <1> 0.0000
13 C9 -2.5398 10.5303 69.3937 C.2 1 <1> 0.0000
14 C10 -1.3667 11.2862 68.9679 C.ar 1 <1> 0.0000
15 C11 -1.1972 12.4947 68.3192 C.ar 1 <1> 0.0000
16 C12 0.1102 12.9236 68.0664 C.ar 1 <1> 0.0000
17 C13 1.2164 12.1476 68.4611 C.ar 1 <1> 0.0000
18 C14 1.0371 10.9278 69.1162 C.ar 1 <1> 0.0000
19 C15 -0.2614 10.5232 69.3557 C.ar 1 <1> 0.0000
20 N2 -0.6741 9.3472 69.9921 N.am 1 <1> 0.0000
21 C16 -2.0689 9.2694 70.0590 C.2 1 <1> 0.0000
22 O2 -2.7654 8.3945 70.5396 O.2 1 <1> 0.0000
23 H3 -0.0323 8.6510 70.3526 H 1 <1> 0.0000
24 H4 1.8782 10.3175 69.4276 H 1 <1> 0.0000
25 Br1 2.9668 12.7687 68.1005 Br 1 <1> 0.0000
26 H5 0.2584 13.8733 67.5569 H 1 <1> 0.0000
27 H6 -2.0419 13.1009 68.0111 H 1 <1> 0.0000
28 N3 -4.9578 10.1672 69.6323 N.pl3 1 <1> 0.0000
29 H7 -4.9443 9.2801 70.1070 H 1 <1> 0.0000
30 H8 -7.7074 9.6340 69.9670 H 1 <1> 0.0000
31 H9 -9.4451 11.2159 69.1536 H 1 <1> 0.0000
32 H10 -8.8087 13.3216 68.0182 H 1 <1> 0.0000
@<TRIPOS>BOND
1 1 6 ar
2 1 2 ar
3 2 3 ar
4 3 4 ar
5 4 28 1
6 4 5 ar
7 5 6 ar
8 6 7 1
9 5 8 1
10 8 9 2
11 9 10 1
12 10 11 1
13 8 12 1
14 12 13 2
15 13 21 1
16 13 14 1
17 14 19 ar
18 14 15 ar
19 15 16 ar
20 16 17 ar
21 17 18 ar
22 18 19 ar
23 19 20 1
24 20 21 am
25 21 22 2
26 20 23 1
27 18 24 1
28 17 25 1
29 16 26 1
30 15 27 1
31 12 28 1
32 28 29 1
33 3 30 1
34 2 31 1
35 1 32 1
@<TRIPOS>SUBSTRUCTURE
1 **** 1 TEMP 0 **** **** 0 ROOT
# Name: 1UV5_extract
# Creating user name: mitya
# Creation time: Wed Sep 22 20:24:49 2010
# Modifying user name: mitya
# Modification time: Wed Sep 22 20:24:49 2010
@<TRIPOS>MOLECULE
1UV5_extract
32 35 1 0 7
SMALL
USER_CHARGES
INVALID_CHARGES
@<TRIPOS>ATOM
1 C1 -5.9361 12.2620 69.3758 C.ar 1 BRW1383 0.0241
2 C2 -4.5220 12.3278 69.0251 C.2 1 BRW1383 0.1287
3 C3 -6.1148 10.9857 70.0838 C.ar 1 BRW1383 0.0724
4 N4 -4.8954 10.3254 70.1260 N.pl3 1 BRW1383 -0.2630
5 C5 -7.3188 10.6018 70.5746 C.ar 1 BRW1383 -0.0386
6 C7 -8.4806 11.5255 70.4000 C.ar 1 BRW1383 -0.0723
7 C9 -8.3202 12.7142 69.7444 C.ar 1 BRW1383 -0.0740
8 C11 -6.9880 13.1155 69.2006 C.ar 1 BRW1383 -0.0644
9 C13 -3.8833 11.1139 69.5150 C.2 1 BRW1383 0.1048
10 C14 -2.6306 10.7061 69.5100 C.2 1 BRW1383 0.0626
11 C15 -2.2182 9.3734 70.0178 C.2 1 BRW1383 0.2013
12 N16 -0.8066 9.2445 69.9057 N.am 1 BRW1383 -0.2437
13 C17 -0.3350 10.4490 69.3901 C.ar 1 BRW1383 0.0647
14 C18 -1.3569 11.3173 69.0963 C.ar 1 BRW1383 -0.0097
15 C19 1.0805 10.7976 69.1632 C.ar 1 BRW1383 -0.0398
16 C20 1.3744 12.0373 68.6822 C.ar 1 BRW1383 -0.0089
17 C21 0.2859 12.9626 68.3524 C.ar 1 BRW1383 -0.0761
18 C22 -1.0032 12.6359 68.5621 C.ar 1 BRW1383 -0.0768
19 O23 -2.9624 8.5003 70.4746 O.2 1 BRW1383 -0.3975
20 N24 -3.9098 13.2420 68.3924 N.2 1 BRW1383 -0.1168
21 O39 -4.3270 14.3749 67.8709 O.3 1 BRW1383 -0.2294
22 BR21 3.1519 12.6181 68.4573 Br 1 BRW1383 -0.0609
23 H1 -4.7449 9.3951 70.5415 H 1 BRW1383 0.2204
24 H2 -7.4358 9.6500 71.0803 H 1 BRW1383 0.0540
25 H3 -9.4527 11.2523 70.7942 H 1 BRW1383 0.0575
26 H4 -9.1706 13.3742 69.6175 H 1 BRW1383 0.0520
27 H5 -6.8597 14.0583 68.6812 H 1 BRW1383 0.0580
28 H6 -0.2589 8.4442 70.1496 H 1 BRW1383 0.2233
29 H7 1.8683 10.0835 69.3744 H 1 BRW1383 0.0505
30 H8 0.5246 13.9320 67.9300 H 1 BRW1383 0.0494
31 H9 -1.7844 13.3522 68.3345 H 1 BRW1383 0.0510
32 H10 -3.5958 14.8244 67.4637 H 1 BRW1383 0.2973
@<TRIPOS>BOND
1 1 8 ar
2 1 3 ar
3 1 2 1
4 2 20 2
5 2 9 1
6 9 10 2
7 9 4 1
8 4 23 1
9 4 3 1
10 3 5 ar
11 5 24 1
12 5 6 ar
13 6 25 1
14 6 7 ar
15 7 26 1
16 7 8 ar
17 8 27 1
18 10 14 1
19 10 11 1
20 11 19 2
21 11 12 am
22 12 28 1
23 12 13 1
24 13 15 ar
25 13 14 ar
26 14 18 ar
27 18 31 1
28 18 17 ar
29 17 30 1
30 17 16 ar
31 16 15 ar
32 16 22 1
33 15 29 1
34 20 21 1
35 21 32 1
@<TRIPOS>SUBSTRUCTURE
1 BRW1383 1 GROUP 0 A **** 0 ROOT BRW A1383
@<TRIPOS>SET
UNK_ATOMS STATIC ATOMS AMSOM **** Atom types guessed for these
atoms
21 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 \
20 21
UNK_AMBER7_FF99 STATIC ATOMS <user> ****
22 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 \
20 21 22
UNK_AMBER7_FF02 STATIC ATOMS <user> ****
22 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 \
20 21 22
UNK_AMBER95_ALL STATIC ATOMS <user> ****
22 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 \
20 21 22
UNK_KOLL_ALL STATIC ATOMS <user> ****
22 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 \
20 21 22
X_ATOM_TYPES STATIC ATOMS <user> **** ""
22 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 \
20 21 22
X_CHARGES STATIC SUBSTS <user> **** ""
1 1
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