Thanks for identifying the problem of NO2 and CO2 functional groups for
acdoctor. We will fix it.
The antechamber program works fine for all the three molecules. We have a
special treatment for NO2 and CO2 in bond type assignment.
For the edited_ecein.mol case, the bond assignment by Antechamber looks
fine to me. After remove all the connection information (antechamber -fi
sdf -fo pdb -i edited_ecein.mol -o edited_ecein.pdb and then remove all the
CONECT fields), antechamber produces same results (antechamber -fi pdb -i
edited_ecein.pdb -fo mol2 -i edited_ecein.mol2).
All the best
Junmei
On Wed, Sep 27, 2017 at 9:18 PM, Scott Brozell <sbrozell.rci.rutgers.edu>
wrote:
> Hi,
>
> Great, thanks for the reports. For future reference you can also
> cc my email with attachments.
>
> thanks,
> scott
>
> On Wed, Sep 27, 2017 at 01:29:13PM -0700, Eric Pettersen wrote:
> > I see now that the edited_ecein.mol, when converted to mol2 (by
> Chimera), has the bond valence marked wrong, but the problem with the nitro
> group stands. Likely due to the limitation of the bond types available in
> mol2 files..
> >
> > ???Eric
> >
> > > On 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.
> > >>
>
> _______________________________________________
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>
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Received on Thu Oct 05 2017 - 09:00:02 PDT
