Dear OpenBabel developers,
I have noticed that the following command
$ obenergy -ff MMFF94 test.sdf
fails assigning proper atom type 48 (NSO) to the appropriate nitrogen
atoms in the test.sdf file attached at the end of this e-mail; the error
message is:
obenergy: could not setup force field.
The attached patch seems to fix the problem with no collateral issues (I
have tested it on the whole MMFF94 validation set); you may wish to
include it in the forthcoming 2.3 release.
Best regards,
Paolo
##### ATTACHMENTS #####
##### test.sdf #####
TEST1
TEST1
23 22 0 0 1 0 0 0 0 0999 V2000
3.6430 9.3360 15.9670 S 0 0 3 0 0 0 0 0 0 0 0 0
2.5020 10.2320 15.9340 O 0 0 0 0 0 0 0 0 0 0 0 0
3.6330 7.9470 15.2960 N 0 0 0 0 0 0 0 0 0 0 0 0
5.0530 10.2190 15.3270 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0640 9.0820 17.6870 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8230 10.3350 18.5340 C 0 0 0 0 0 0 0 0 0 0 0 0
4.7010 10.3640 19.7740 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1030 11.3320 20.7820 N 0 0 0 0 0 0 0 0 0 0 0 0
6.1610 10.8340 19.4750 C 0 0 0 0 0 0 0 0 0 0 0 0
6.6680 10.4900 18.3860 O 0 0 0 0 0 0 0 0 0 0 0 0
6.5560 11.5890 20.4210 O 0 0 0 0 0 0 0 0 0 0 0 0
2.8040 7.4110 15.5590 H 0 0 0 0 0 0 0 0 0 0 0 0
5.9490 9.6110 15.4640 H 0 0 0 0 0 0 0 0 0 0 0 0
5.1490 11.1680 15.8570 H 0 0 0 0 0 0 0 0 0 0 0 0
4.8820 10.4100 14.2650 H 0 0 0 0 0 0 0 0 0 0 0 0
5.0950 8.7210 17.7140 H 0 0 0 0 0 0 0 0 0 0 0 0
3.4240 8.2720 18.0550 H 0 0 0 0 0 0 0 0 0 0 0 0
4.0060 11.2430 17.9450 H 0 0 0 0 0 0 0 0 0 0 0 0
2.7620 10.3620 18.8130 H 0 0 0 0 0 0 0 0 0 0 0 0
4.7340 9.3950 20.2830 H 0 0 0 0 0 0 0 0 0 0 0 0
4.9810 11.7050 21.2270 H 0 0 0 0 0 0 0 0 0 0 0 0
3.5150 10.9120 21.5000 H 0 0 0 0 0 0 0 0 0 0 0 0
3.6860 12.1540 20.3370 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
1 3 2 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
3 12 1 0 0 0 0
4 13 1 0 0 0 0
4 14 1 0 0 0 0
4 15 1 0 0 0 0
5 6 1 0 0 0 0
5 16 1 0 0 0 0
5 17 1 0 0 0 0
6 7 1 0 0 0 0
6 18 1 0 0 0 0
6 19 1 0 0 0 0
7 8 1 0 0 0 0
7 9 1 0 0 0 0
7 20 1 0 0 0 0
8 21 1 0 0 0 0
8 22 1 0 0 0 0
8 23 1 0 0 0 0
9 10 2 0 0 0 0
9 11 1 0 0 0 0
M END
$$$$
TEST2
TEST2
26 27 0 0 1 0 0 0 0 0999 V2000
0.8740 2.9590 0.7490 S 0 0 3 0 0 0 0 0 0 0 0 0
1.0730 1.6580 0.1410 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.7560 4.8570 -1.7030 O 0 0 0 0 0 0 0 0 0 0 0 0
1.1860 5.4700 -0.7410 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.2170 3.9610 0.3550 N 0 0 0 0 0 0 0 0 0 0 0 0
0.7470 2.6930 2.5080 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3310 1.5510 3.0640 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2510 1.3370 4.4410 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5840 2.2560 5.2530 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0100 3.3870 4.6920 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0660 3.6090 3.3160 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0130 4.7590 -0.7600 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0520 5.3190 0.4040 C 0 0 3 0 0 0 0 0 0 0 0 0
2.4060 3.8530 0.5900 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3020 6.1490 0.1410 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8390 0.8210 2.4380 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6980 0.4490 4.8800 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5160 2.0820 6.3240 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.5440 4.0900 5.3270 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.4200 4.4840 2.8920 H 0 0 0 0 0 0 0 0 0 0 0 0
1.5430 5.7310 1.2850 H 0 0 0 0 0 0 0 0 0 0 0 0
3.0360 3.6750 1.4650 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9060 3.4530 -0.2990 H 0 0 0 0 0 0 0 0 0 0 0 0
3.0350 7.2000 -0.0150 H 0 0 0 0 0 0 0 0 0 0 0 0
4.0030 6.0870 0.9800 H 0 0 0 0 0 0 0 0 0 0 0 0
3.8120 5.8160 -0.7690 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
1 5 2 0 0 0 0
1 6 1 0 0 0 0
1 14 1 0 0 0 0
3 12 2 0 0 0 0
4 12 1 0 0 0 0
4 13 1 0 0 0 0
5 12 1 0 0 0 0
6 7 1 0 0 0 0
6 11 2 0 0 0 0
7 8 2 0 0 0 0
7 16 1 0 0 0 0
8 9 1 0 0 0 0
8 17 1 0 0 0 0
9 10 2 0 0 0 0
9 18 1 0 0 0 0
10 11 1 0 0 0 0
10 19 1 0 0 0 0
11 20 1 0 0 0 0
13 14 1 0 0 0 0
13 15 1 0 0 0 0
13 21 1 0 0 0 0
14 22 1 0 0 0 0
14 23 1 0 0 0 0
15 24 1 0 0 0 0
15 25 1 0 0 0 0
15 26 1 0 0 0 0
M END
$$$$
TEST3
TEST3
21 21 0 0 0 0 0 0 0 0999 V2000
1.7960 1.3130 7.9490 S 0 0 0 0 0 0 0 0 0 0 0 0
1.4860 0.8970 6.2780 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2130 1.1310 5.9570 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5630 1.6810 7.0490 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1450 1.8480 8.1680 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7730 0.2960 5.3600 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-0.4490 0.8410 4.4040 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-2.2170 2.0950 6.8950 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-0.2920 2.4710 9.6780 Cl 0 0 0 0 0 0 0 0 0 0 0 0
2.8680 2.4060 8.1590 N 0 0 0 0 0 0 0 0 0 0 0 0
2.8020 3.6210 7.5010 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9110 3.9210 6.7170 O 0 0 0 0 0 0 0 0 0 0 0 0
3.8370 4.4330 7.8270 O 0 0 0 0 0 0 0 0 0 0 0 0
3.8250 5.7060 7.1760 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0370 6.4890 7.6420 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8910 0.0430 8.6560 O 0 0 0 0 0 0 0 0 0 0 0 0
3.8700 5.5680 6.0900 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9100 6.2490 7.4420 H 0 0 0 0 0 0 0 0 0 0 0 0
5.0700 7.4750 7.1690 H 0 0 0 0 0 0 0 0 0 0 0 0
5.9590 5.9500 7.4020 H 0 0 0 0 0 0 0 0 0 0 0 0
5.0170 6.6190 8.7290 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
1 10 2 0 0 0 0
1 16 2 0 0 0 0
2 3 2 0 0 0 0
2 6 1 0 0 0 0
3 4 1 0 0 0 0
3 7 1 0 0 0 0
4 5 2 0 0 0 0
4 8 1 0 0 0 0
5 9 1 0 0 0 0
10 11 1 0 0 0 0
11 12 2 0 0 0 0
11 13 1 0 0 0 0
13 14 1 0 0 0 0
14 15 1 0 0 0 0
14 17 1 0 0 0 0
14 18 1 0 0 0 0
15 19 1 0 0 0 0
15 20 1 0 0 0 0
15 21 1 0 0 0 0
M END
$$$$
##### PATCH #####
*** src/forcefields/forcefieldmmff94.cpp 2010-09-23
18:05:15.000000000 +0200
--- src/forcefields/forcefieldmmff94.cpp 2010-09-23
18:09:39.000000000 +0200
***************
*** 2191,2197 ****
}
}
! if (atom->BOSum() == 2) {
oxygenCount = sulphurCount = 0;
FOR_NBORS_OF_ATOM (nbr, atom) {
--- 2191,2197 ----
}
}
! if (atom->BOSum() >= 2) {
oxygenCount = sulphurCount = 0;
FOR_NBORS_OF_ATOM (nbr, atom) {
--
================================================================
Paolo Tosco, Ph.D. Phone: +39 011 6707680
Dipartimento di Scienza Fax: +39 011 6707687
e Tecnologia del Farmaco Mob: +39 348 5537206
Via Pietro Giuria, 9 E-mail: [email protected]
I-10125 Torino
Italy http://www.open3dqsar.org
================================================================
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