I'll add that carboxylates also cause problems for acdoctor. For example,
this command ...
> antechamber -i kt1.mol2 -fi mol2 -o tmp.mol2 -fo mol2 -at sybyl -c bcc
-nc -1
... produces "Weird atomic valence" for the mol2 file below. I think
acdoctor doesn't like that the C-O bond types for the carboxylate are
listed as single bonds. Obviously there is hybridization going on, but the
mol2 format doesn't have a type for that situation, so single bond is the
only sensible thing to use.
--Niel
### kt1.mol2
.<TRIPOS>MOLECULE
KT1
17 16 1 0 0
SMALL
No Charge or Current Charge
.<TRIPOS>ATOM
1 C 0.0000 0.0000 0.0000 C.3 1 KT1
0.000000
2 N 1.4480 -0.0000 0.0000 N.am 1 KT1
0.000000
3 H -0.3640 1.0270 0.0000 H 1 KT1
0.000000
4 H1 -0.3630 -0.5140 -0.8900 H 1 KT1
0.000000
5 H2 -0.3630 -0.5140 0.8900 H 1 KT1
0.000000
6 H3 1.9530 0.8750 0.0000 H 1 KT1
0.000000
7 C1 2.1710 -1.2540 -0.0000 C.2 1 KT1
0.000000
8 C2 3.6960 -1.2540 0.0000 C.3 1 KT1
0.000000
9 O 1.5520 -2.3260 -0.0000 O.2 1 KT1
0.000000
10 C3 4.2050 -2.6910 -0.0000 C.3 1 KT1
0.000000
11 H4 4.0590 -0.7400 -0.8900 H 1 KT1
0.000000
12 H5 4.0590 -0.7400 0.8900 H 1 KT1
0.000000
13 C4 5.7290 -2.6910 -0.0000 C.2 1 KT1
0.000000
14 H6 3.8420 -3.2040 0.8900 H 1 KT1
0.000000
15 H7 3.8410 -3.2050 -0.8900 H 1 KT1
0.000000
16 O1 6.3480 -1.6180 0.0000 O.co2 1 KT1
0.000000
17 O2 6.3480 -3.7630 -0.0000 O.co2 1 KT1
0.000000
.<TRIPOS>BOND
1 1 2 1
2 1 3 1
3 1 4 1
4 1 5 1
5 2 6 1
6 2 7 am
7 7 8 1
8 7 9 2
9 8 10 1
10 8 11 1
11 8 12 1
12 10 13 1
13 10 14 1
14 10 15 1
15 13 16 1
16 13 17 1
.<TRIPOS>SUBSTRUCTURE
1 KT1 1 TEMP 0 **** **** 0 ROOT
On Wed, Sep 27, 2017 at 12:49 PM, Eric Pettersen <pett.cgl.ucsf.edu> wrote:
> The mailing list seems to have stripped my attachments, so I guess I’m
> forced to paste in the full text of the files. Here goes:
>
> nitro.mol2
> ——————
> .<TRIPOS>MOLECULE
> smiles:C1=CC2=C(C=CC=...
> 19 20 1 0 0
> SMALL
> AMBER ff14SB
>
>
> .<TRIPOS>ATOM
> 1 C1 2.8006 6.3718 8.4116 C.ar 1 UNK 0.0000
> 2 C2 3.9242 6.4284 7.5826 C.ar 1 UNK 0.0000
> 3 C3 4.2908 5.3773 6.7484 C.ar 1 UNK 0.0000
> 4 C4 3.5096 4.2025 6.7330 C.ar 1 UNK 0.0000
> 5 C5 3.9277 3.1781 5.8472 C.ar 1 UNK 0.0000
> 6 C6 5.0575 3.3439 5.0550 C.ar 1 UNK 0.0000
> 7 C7 5.7469 4.5322 5.1599 C.ar 1 UNK 0.0000
> 8 N1 5.3826 5.5374 5.9833 N.ar 1 UNK 0.0000
> 9 C8 2.3772 4.1606 7.5898 C.ar 1 UNK 0.0000
> 10 C9 2.0148 5.2300 8.4180 C.ar 1 UNK 0.0000
> 11 N2 1.5307 2.9821 7.6362 N.2 1 UNK 0.0000
> 12 O1 0.3286 3.1441 7.3871 O.co2 1 UNK 0.0000
> 13 O2 2.0632 1.9073 7.9428 O.co2 1 UNK 0.0000
> 14 H1 2.5490 7.2200 9.0438 H 1 UNK 0.0000
> 15 H2 4.5369 7.3290 7.5818 H 1 UNK 0.0000
> 16 H3 3.3815 2.2404 5.7663 H 1 UNK 0.0000
> 17 H4 5.3886 2.5654 4.3770 H 1 UNK 0.0000
> 18 H5 6.6382 4.7195 4.5675 H 1 UNK 0.0000
> 19 H6 1.1370 5.1760 9.0585 H 1 UNK 0.0000
> .<TRIPOS>BOND
> 1 1 2 ar
> 2 1 10 ar
> 3 1 14 1
> 4 2 3 ar
> 5 2 15 1
> 6 3 4 ar
> 7 3 8 ar
> 8 4 5 ar
> 9 4 9 ar
> 10 5 6 ar
> 11 5 16 1
> 12 6 7 ar
> 13 6 17 1
> 14 7 8 ar
> 15 7 18 1
> 16 9 10 ar
> 17 9 11 1
> 18 10 19 1
> 19 11 12 2
> 20 11 13 2
> .<TRIPOS>SUBSTRUCTURE
> 1 UNK 1 RESIDUE 4 A UNK 0 ROOT
>
>
> edited_ecein.mol:
> ————————————
> edited_ecein.mol
> OpenBabel09261710393D
>
> 110113 0 0 1 0 0 0 0 0999 V2000
> 193.7820 -7.7740 -6.9300 C 0 0 0 0 0 0 0 0 0 0 0 0
> 193.8620 -8.2090 -7.9260 H 0 0 0 0 0 0 0 0 0 0 0 0
> 194.6570 -7.1600 -6.7210 H 0 0 0 0 0 0 0 0 0 0 0 0
> 192.8720 -7.1750 -6.8810 H 0 0 0 0 0 0 0 0 0 0 0 0
> 193.7560 -8.8580 -5.9950 O 0 0 0 0 0 0 0 0 0 0 0 0
> 193.6620 -8.4980 -4.6130 C 0 0 2 0 0 0 0 0 0 0 0 0
> 193.9160 -9.3810 -4.0280 H 0 0 0 0 0 0 0 0 0 0 0 0
> 192.2150 -8.0660 -4.3570 C 0 0 0 0 0 0 0 0 0 0 0 0
> 192.0230 -7.0920 -4.8070 H 0 0 0 0 0 0 0 0 0 0 0 0
> 192.0250 -8.0090 -3.2860 H 0 0 0 0 0 0 0 0 0 0 0 0
> 191.5390 -8.8050 -4.7850 H 0 0 0 0 0 0 0 0 0 0 0 0
> 194.6780 -7.3910 -4.3080 C 0 0 2 0 0 0 0 0 0 0 0 0
> 194.9090 -7.1450 -2.8190 C 0 0 2 0 0 0 0 0 0 0 0 0
> 195.4780 -6.2210 -2.7270 H 0 0 0 0 0 0 0 0 0 0 0 0
> 195.5890 -8.2240 -2.1430 O 0 0 0 0 0 0 0 0 0 0 0 0
> 193.5690 -6.8800 -2.1310 C 0 0 0 0 0 0 0 0 0 0 0 0
> 193.7400 -6.4680 -1.1370 H 0 0 0 0 0 0 0 0 0 0 0 0
> 193.0020 -7.8040 -2.0340 H 0 0 0 0 0 0 0 0 0 0 0 0
> 193.0200 -6.1550 -2.7340 H 0 0 0 0 0 0 0 0 0 0 0 0
> 194.2320 -6.1670 -4.9110 O 0 0 0 0 0 0 0 0 0 0 0 0
> 193.3070 -5.9550 -4.5970 H 0 0 0 0 0 0 0 0 0 0 0 0
> 196.0230 -7.7820 -4.8980 C 0 0 0 0 0 0 0 0 0 0 0 0
> 196.7300 -6.9930 -4.6440 H 0 0 0 0 0 0 0 0 0 0 0 0
> 195.9740 -7.9780 -5.9690 H 0 0 0 0 0 0 0 0 0 0 0 0
> 196.4650 -9.0560 -4.2020 C 0 0 0 0 0 0 0 0 0 0 0 0
> 195.6580 -9.7890 -4.2130 H 0 0 0 0 0 0 0 0 0 0 0 0
> 197.2770 -9.5340 -4.7470 H 0 0 0 0 0 0 0 0 0 0 0 0
> 196.7930 -8.7200 -2.7570 C 0 0 1 0 0 0 0 0 0 0 0 0
> 197.1040 -9.6420 -2.2640 H 0 0 0 0 0 0 0 0 0 0 0 0
> 197.9490 -7.7300 -2.6560 C 0 0 1 0 0 0 0 0 0 0 0 0
> 199.0230 -8.0840 -3.6940 C 0 0 0 0 0 0 0 0 0 0 0 0
> 199.7250 -7.2830 -3.9280 H 0 0 0 0 0 0 0 0 0 0 0 0
> 198.5570 -8.3250 -4.6480 H 0 0 0 0 0 0 0 0 0 0 0 0
> 199.6940 -9.3780 -3.2290 C 0 0 0 0 0 0 0 0 0 0 0 0
> 200.4670 -9.8040 -3.8680 H 0 0 0 0 0 0 0 0 0 0 0 0
> 198.9030 -10.1270 -3.1950 H 0 0 0 0 0 0 0 0 0 0 0 0
> 200.1910 -9.2350 -2.2700 H 0 0 0 0 0 0 0 0 0 0 0 0
> 197.4300 -6.3850 -2.6470 O 0 0 0 0 0 0 0 0 0 0 0 0
> 198.5640 -7.8700 -1.2710 C 0 0 0 0 0 0 0 0 0 0 0 0
> 198.7290 -8.9230 -1.0480 H 0 0 0 0 0 0 0 0 0 0 0 0
> 199.4840 -7.3010 -1.1610 H 0 0 0 0 0 0 0 0 0 0 0 0
> 197.4580 -7.2580 -0.4450 C 0 0 0 0 0 0 0 0 0 0 0 0
> 196.5860 -7.9110 -0.4600 H 0 0 0 0 0 0 0 0 0 0 0 0
> 197.7600 -6.9280 0.5480 H 0 0 0 0 0 0 0 0 0 0 0 0
> 197.1960 -6.0110 -1.2710 C 0 0 1 0 0 0 0 0 0 0 0 0
> 196.1860 -5.7480 -0.9600 H 0 0 0 0 0 0 0 0 0 0 0 0
> 198.1560 -4.9070 -0.8170 C 0 0 2 0 0 0 0 0 0 0 0 0
> 199.4820 -4.9330 -1.5840 C 0 0 0 0 0 0 0 0 0 0 0 0
> 200.0550 -4.0620 -1.2680 H 0 0 0 0 0 0 0 0 0 0 0 0
> 199.3270 -4.9000 -2.6620 H 0 0 0 0 0 0 0 0 0 0 0 0
> 200.0090 -5.8630 -1.3720 H 0 0 0 0 0 0 0 0 0 0 0 0
> 198.4380 -5.0750 0.5740 O 0 0 0 0 0 0 0 0 0 0 0 0
> 197.5920 -4.9900 1.1000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 197.4740 -3.5510 -1.0090 C 0 0 0 0 0 0 0 0 0 0 0 0
> 196.2500 -3.4450 -1.0710 O 0 0 0 0 0 0 0 0 0 0 0 0
> 198.3950 -2.3320 -1.1150 C 0 0 1 0 0 0 0 0 0 0 0 0
> 199.1680 -2.4700 -1.8710 H 0 0 0 0 0 0 0 0 0 0 0 0
> 197.5650 -1.0850 -1.4300 C 0 0 0 0 0 0 0 0 0 0 0 0
> 198.2010 -0.2000 -1.4690 H 0 0 0 0 0 0 0 0 0 0 0 0
> 196.8260 -0.9240 -0.6450 H 0 0 0 0 0 0 0 0 0 0 0 0
> 196.8460 -1.2660 -2.7680 C 0 0 0 0 0 0 0 0 0 0 0 0
> 197.5740 -1.3990 -3.5680 H 0 0 0 0 0 0 0 0 0 0 0 0
> 196.2410 -0.3830 -2.9780 H 0 0 0 0 0 0 0 0 0 0 0 0
> 196.2010 -2.1430 -2.7110 H 0 0 0 0 0 0 0 0 0 0 0 0
> 199.1840 -2.1510 0.1880 C 0 0 2 0 0 0 0 0 0 0 0 0
> 199.1550 -3.1210 0.6820 H 0 0 0 0 0 0 0 0 0 0 0 0
> 198.5950 -1.1270 0.9940 O 0 0 0 0 0 0 0 0 0 0 0 0
> 199.1780 -0.9450 1.7850 H 0 0 0 0 0 0 0 0 0 0 0 0
> 200.6160 -1.7700 -0.2100 C 0 0 1 0 0 0 0 0 0 0 0 0
> 201.0480 -2.5720 -0.8070 H 0 0 0 0 0 0 0 0 0 0 0 0
> 200.5250 -0.5980 -1.1900 C 0 0 0 0 0 0 0 0 0 0 0 0
> 200.0780 -0.9430 -2.1220 H 0 0 0 0 0 0 0 0 0 0 0 0
> 201.5300 -0.2340 -1.4000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 199.9470 0.2130 -0.7490 H 0 0 0 0 0 0 0 0 0 0 0 0
> 201.5490 -1.2490 0.8870 C 0 0 2 0 0 0 0 0 0 0 0 0
> 201.3540 -0.1770 0.9280 H 0 0 0 0 0 0 0 0 0 0 0 0
> 202.8990 -1.5340 0.4900 O 0 0 0 0 0 0 0 0 0 0 0 0
> 201.3430 -1.7630 2.3010 C 0 0 1 0 0 0 0 0 0 0 0 0
> 200.3310 -1.6470 2.6900 H 0 0 0 0 0 0 0 0 0 0 0 0
> 201.7300 -3.2160 2.5860 C 0 0 0 0 0 0 0 0 0 0 0 0
> 201.6500 -3.2700 3.6730 H 0 0 0 0 0 0 0 0 0 0 0 0
> 202.7190 -3.5020 2.2270 H 0 0 0 0 0 0 0 0 0 0 0 0
> 201.1280 -3.9660 2.0730 H 0 0 0 0 0 0 0 0 0 0 0 0
> 202.2920 -0.9380 3.1600 C 0 0 0 0 0 0 0 0 0 0 0 0
> 202.1480 0.1290 2.9850 H 0 0 0 0 0 0 0 0 0 0 0 0
> 202.1150 -1.1620 4.2110 H 0 0 0 0 0 0 0 0 0 0 0 0
> 203.7270 -1.2320 2.7420 C 0 0 2 0 0 0 0 0 0 0 0 0
> 203.9780 -2.2840 2.8650 H 0 0 0 0 0 0 0 0 0 0 0 0
> 204.7400 -0.4700 3.5980 C 0 0 0 0 0 0 0 0 0 0 0 0
> 204.7410 -0.8740 4.6100 H 0 0 0 0 0 0 0 0 0 0 0 0
> 204.4970 0.5900 3.6670 H 0 0 0 0 0 0 0 0 0 0 0 0
> 205.7300 -0.7070 3.2060 H 0 0 0 0 0 0 0 0 0 0 0 0
> 203.8970 -0.8630 1.2740 C 0 0 2 0 0 0 0 0 0 0 0 0
> 204.8620 -1.1640 0.8670 H 0 0 0 0 0 0 0 0 0 0 0 0
> 203.7310 0.6340 1.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 202.8870 1.0950 1.5130 H 0 0 0 0 0 0 0 0 0 0 0 0
> 203.4270 0.7630 -0.0390 H 0 0 0 0 0 0 0 0 0 0 0 0
> 204.9410 1.4650 1.4360 C 0 0 0 0 0 0 0 0 0 0 0 0
> 204.8910 2.1160 2.4770 O 0 0 0 0 0 0 0 0 0 0 0 0
> 206.0290 1.5250 0.6710 C 0 0 1 0 0 0 0 0 0 0 0 0
> 206.2790 0.9420 -0.4970 C 0 0 0 0 0 0 0 0 0 0 0 0
> 205.5200 0.1920 -1.1100 O 0 0 0 0 0 0 0 0 0 0 0 0
> 207.5250 1.3250 -0.8960 O 0 0 0 0 0 0 0 0 0 0 0 0
> 208.0120 2.1540 0.0720 C 0 0 0 0 0 0 0 0 0 0 0 0
> 209.2010 2.7480 0.0710 C 0 0 0 0 0 0 0 0 0 0 0 0
> 209.9560 2.6080 -0.7040 H 0 0 0 0 0 0 0 0 0 0 0 0
> 209.5250 3.2340 0.9920 H 0 0 0 0 0 0 0 0 0 0 0 0
> 207.0820 2.2620 1.0180 C 0 0 0 0 0 0 0 0 0 0 0 0
> 207.1900 3.0040 2.1520 O 0 0 0 0 0 0 0 0 0 0 0 0
> 206.3590 2.9090 2.6990 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 4 1 0 0 0 0
> 1 3 1 0 0 0 0
> 1 5 1 0 0 0 0
> 2 1 1 0 0 0 0
> 5 6 1 0 0 0 0
> 6 8 1 0 0 0 0
> 6 12 1 0 0 0 0
> 6 7 1 1 0 0 0
> 8 10 1 0 0 0 0
> 9 8 1 0 0 0 0
> 11 8 1 0 0 0 0
> 12 20 1 6 0 0 0
> 12 13 1 0 0 0 0
> 13 14 1 1 0 0 0
> 13 15 1 0 0 0 0
> 13 16 1 0 0 0 0
> 16 18 1 0 0 0 0
> 16 17 1 0 0 0 0
> 19 16 1 0 0 0 0
> 20 21 1 0 0 0 0
> 22 23 1 0 0 0 0
> 22 12 1 0 0 0 0
> 22 25 1 0 0 0 0
> 24 22 1 0 0 0 0
> 25 28 1 0 0 0 0
> 26 25 1 0 0 0 0
> 27 25 1 0 0 0 0
> 28 30 1 0 0 0 0
> 28 29 1 1 0 0 0
> 28 15 1 0 0 0 0
> 30 31 1 6 0 0 0
> 30 38 1 0 0 0 0
> 30 39 1 0 0 0 0
> 31 34 1 0 0 0 0
> 32 31 1 0 0 0 0
> 33 31 1 0 0 0 0
> 34 36 1 0 0 0 0
> 34 37 1 0 0 0 0
> 35 34 1 0 0 0 0
> 38 45 1 0 0 0 0
> 39 41 1 0 0 0 0
> 39 40 1 0 0 0 0
> 39 42 1 0 0 0 0
> 42 44 1 0 0 0 0
> 43 42 1 0 0 0 0
> 45 46 1 1 0 0 0
> 45 47 1 0 0 0 0
> 45 42 1 0 0 0 0
> 47 48 1 6 0 0 0
> 47 52 1 0 0 0 0
> 48 51 1 0 0 0 0
> 48 49 1 0 0 0 0
> 50 48 1 0 0 0 0
> 52 53 1 0 0 0 0
> 54 47 1 0 0 0 0
> 55 54 2 0 0 0 0
> 56 57 1 6 0 0 0
> 56 54 1 0 0 0 0
> 56 65 1 0 0 0 0
> 58 56 1 0 0 0 0
> 58 60 1 0 0 0 0
> 59 58 1 0 0 0 0
> 61 64 1 0 0 0 0
> 61 58 1 0 0 0 0
> 62 61 1 0 0 0 0
> 63 61 1 0 0 0 0
> 65 66 1 1 0 0 0
> 65 67 1 0 0 0 0
> 67 68 1 0 0 0 0
> 69 70 1 6 0 0 0
> 69 65 1 0 0 0 0
> 69 75 1 0 0 0 0
> 71 74 1 0 0 0 0
> 71 69 1 0 0 0 0
> 72 71 1 0 0 0 0
> 73 71 1 0 0 0 0
> 75 76 1 1 0 0 0
> 75 78 1 0 0 0 0
> 77 75 1 0 0 0 0
> 77 93 1 0 0 0 0
> 78 80 1 0 0 0 0
> 78 79 1 1 0 0 0
> 78 84 1 0 0 0 0
> 80 81 1 0 0 0 0
> 82 80 1 0 0 0 0
> 83 80 1 0 0 0 0
> 84 86 1 0 0 0 0
> 85 84 1 0 0 0 0
> 87 88 1 1 0 0 0
> 87 84 1 0 0 0 0
> 87 89 1 0 0 0 0
> 89 91 1 0 0 0 0
> 89 90 1 0 0 0 0
> 92 89 1 0 0 0 0
> 93 94 1 6 0 0 0
> 93 87 1 0 0 0 0
> 95 93 1 0 0 0 0
> 95 98 1 0 0 0 0
> 95 96 1 0 0 0 0
> 97 95 1 0 0 0 0
> 98 99 2 0 0 0 0
> 100108 1 0 0 0 0
> 100 98 1 6 0 0 0
> 101100 1 0 0 0 0
> 102101 2 0 0 0 0
> 103101 1 0 0 0 0
> 103104 1 0 0 0 0
> 104108 2 0 0 0 0
> 105104 1 0 0 0 0
> 105107 1 0 0 0 0
> 106105 1 0 0 0 0
> 108109 1 0 0 0 0
> 109110 1 0 0 0 0
> M END
>
> > On Sep 27, 2017, at 12:43 PM, Eric Pettersen <pett.cgl.ucsf.edu> wrote:
> >
> > Antechamber’s new “acdoctor” sometimes misdiagnoses valences and rejects
> perfectly fine compounds. I am currently working around the issue by
> turning off the doctor with the “-dr n” flag, but thought I would provide a
> couple of examples of bad diagnoses so that hopefully acdoctor can be
> improved.
> >
> > The first is pretty simple. It believes a nitro group implies 5 bonds
> to the nitrogen rather than 4, e.g. N2 in this compound:
> >
> >
> >
> > The second is a misdiagnosis of the valences in/near a ring. In the
> following compound it believes there is a double bond between C33 and C34
> (giving C33 a valence of 5) when the double bond is actually between C34
> and C38.
> >
> >
> >
> > —Eric
> >
> >
> > Eric Pettersen
> > UCSF Computer Graphics Lab
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 27 2017 - 13:30:03 PDT
