Closed missuse closed 2 years ago
Hi,
EDIT: issue is resolved, I should have used sdf (mol) format instead of mol2. Sorry to waste your time.
Initial problem:
I am trying to convert NADP from mol2 to pdbqt,
mk_prepare_ligand.py -i NADP.mol2 -o NADP.pdbqt
however I get the warning:
[16:15:43] NADP: warning - O.co2 with non C.2 or S.o2 neighbor.
I guess this is related to the phosphate groups:
https://github.com/rdkit/rdkit/issues/3246 https://github.com/rdkit/rdkit/issues/1806
I would be grateful for any suggestion on how to proceed?
All the best,
Milan
NADP.mol2:
@<TRIPOS>MOLECULE NADP 73 77 0 0 0 SMALL GASTEIGER @<TRIPOS>ATOM 1 P 0.0400 5.3860 -0.1340 P.3 1 NADP 0.2182 2 O 1.2730 6.0120 0.3750 O.co2 1 NADP -0.4371 3 O 0.1690 4.7430 -1.4530 O.2 1 NADP -0.5170 4 O -1.2060 6.3690 -0.1190 O.3 1 NADP -0.3246 5 C -1.5090 7.1140 1.0330 C.3 1 NADP 0.0836 6 C -2.7900 7.8730 0.7340 C.3 1 NADP 0.1133 7 O -3.3120 8.4770 1.9020 O.3 1 NADP -0.3456 8 C -2.5710 9.0030 -0.2830 C.3 1 NADP 0.1141 9 O -3.7390 9.1680 -1.0600 O.3 1 NADP -0.3864 10 C -2.4030 10.2360 0.5640 C.3 1 NADP 0.1351 11 O -2.7420 11.4140 -0.1630 O.3 1 NADP -0.3569 12 C -3.3620 9.8900 1.7120 C.3 1 NADP 0.1672 13 N -3.0200 10.5350 2.9890 N.ar 1 NADP -0.2855 14 C -1.8160 10.5150 3.6750 C.ar 1 NADP 0.1004 15 N -1.9900 11.2070 4.8310 N.ar 1 NADP -0.2306 16 C -3.2750 11.6530 4.8680 C.ar 1 NADP 0.1473 17 C -3.9810 12.4160 5.7900 C.ar 1 NADP 0.1472 18 N -3.3700 12.8560 6.8790 N.pl3 1 NADP -0.3413 19 N -5.3080 12.7170 5.5540 N.ar 1 NADP -0.2188 20 C -5.9440 12.2720 4.4020 C.ar 1 NADP 0.1205 21 N -5.2290 11.5080 3.4860 N.ar 1 NADP -0.2159 22 C -3.9300 11.2200 3.7240 C.ar 1 NADP 0.1674 23 O -0.3830 4.2530 1.0070 O.3 1 NADP -0.2703 24 P -0.3840 2.6060 0.9830 P.3 1 NADP 0.2182 25 O -1.4650 2.1370 0.0490 O.2 1 NADP -0.5170 26 O 1.0140 2.1800 0.8190 O.co2 1 NADP -0.4371 27 O -1.1360 2.2570 2.3560 O.3 1 NADP -0.3246 28 C -0.5580 2.3320 3.5900 C.3 1 NADP 0.0836 29 C -0.6770 0.9790 4.2760 C.3 1 NADP 0.1133 30 O -0.3830 -0.1230 3.4040 O.3 1 NADP -0.3457 31 C 0.4050 1.0580 5.3350 C.3 1 NADP 0.1135 32 O -0.0020 0.4350 6.5150 O.3 1 NADP -0.3864 33 C 1.5440 0.3870 4.6150 C.3 1 NADP 0.1285 34 O 2.5410 0.0130 5.5290 O.3 1 NADP -0.3847 35 C 0.7980 -0.7360 3.8850 C.3 1 NADP 0.1640 36 N 1.6470 -1.4190 2.8760 N.ar 1 NADP -0.3248 37 C 2.1810 -0.7490 1.7980 C.ar 1 NADP 0.0192 38 C 3.0200 -1.4270 0.9020 C.ar 1 NADP 0.0527 39 C 3.4390 -0.7740 -0.3900 C.2 1 NADP 0.2429 40 O 4.3480 -1.4520 -1.2280 O.2 1 NADP -0.2704 41 N 2.9240 0.4280 -0.6980 N.am 1 NADP -0.3253 42 C 3.3020 -2.7750 1.1090 C.ar 1 NADP -0.0469 43 C 2.7610 -3.4290 2.2120 C.ar 1 NADP -0.0447 44 C 1.9460 -2.7390 3.0900 C.ar 1 NADP 0.0071 45 P -2.2410 12.8770 0.3360 P.3 1 NADP -0.0144 46 O -0.7700 12.8060 0.6190 O.co2 1 NADP -0.5770 47 O -3.0440 13.2720 1.5500 O.co2 1 NADP -0.5770 48 O -2.5540 13.8830 -0.7480 O.2 1 NADP -0.6377 49 H -0.7158 7.7989 1.2490 H 1 NADP 0.0591 50 H -1.6275 6.4770 1.8845 H 1 NADP 0.0591 51 H -3.4674 7.1453 0.3384 H 1 NADP 0.0647 52 H -1.7438 8.8099 -0.9336 H 1 NADP 0.0648 53 H -4.4936 9.3435 -0.4763 H 1 NADP 0.2100 54 H -1.4101 10.4581 0.8953 H 1 NADP 0.0671 55 H -4.3328 10.2454 1.4360 H 1 NADP 0.0867 56 H -0.9449 10.0573 3.3640 H 1 NADP 0.1030 57 H -2.4236 12.6346 7.0359 H 1 NADP 0.1438 58 H -3.8620 13.4046 7.5319 H 1 NADP 0.1438 59 H -6.9341 12.5053 4.2282 H 1 NADP 0.1048 60 H -1.0569 3.0760 4.1752 H 1 NADP 0.0591 61 H 0.4738 2.5972 3.4903 H 1 NADP 0.0591 62 H -1.6702 0.8059 4.6344 H 1 NADP 0.0647 63 H 0.6631 2.0380 5.6784 H 1 NADP 0.0647 64 H -0.2652 -0.4789 6.3240 H 1 NADP 0.2100 65 H 2.1093 0.9740 3.9216 H 1 NADP 0.0665 66 H 2.1506 -0.5366 6.2264 H 1 NADP 0.2101 67 H 0.5375 -1.5584 4.5180 H 1 NADP 0.0865 68 H 1.9644 0.2491 1.6499 H 1 NADP 0.0817 69 H 3.1828 0.8742 -1.5366 H 1 NADP 0.1453 70 H 2.2878 0.8626 -0.0851 H 1 NADP 0.1453 71 H 3.9085 -3.2859 0.4485 H 1 NADP 0.0626 72 H 2.9678 -4.4270 2.3741 H 1 NADP 0.0632 73 H 1.5588 -3.2231 3.9151 H 1 NADP 0.0810 @<TRIPOS>BOND 1 3 1 2 2 40 39 2 3 9 8 1 4 48 45 2 5 41 39 am 6 39 38 1 7 8 10 1 8 8 6 1 9 11 45 1 10 11 10 1 11 1 4 1 12 1 2 1 13 1 23 1 14 4 5 1 15 25 24 2 16 45 46 1 17 45 47 1 18 10 12 1 19 6 5 1 20 6 7 1 21 26 24 1 22 38 42 ar 23 38 37 ar 24 24 23 1 25 24 27 1 26 42 43 ar 27 12 7 1 28 12 13 1 29 37 36 ar 30 43 44 ar 31 27 28 1 32 36 44 ar 33 36 35 1 34 13 14 ar 35 13 22 ar 36 30 35 1 37 30 29 1 38 21 22 ar 39 21 20 ar 40 28 29 1 41 14 15 ar 42 22 16 ar 43 35 33 1 44 29 31 1 45 20 19 ar 46 33 31 1 47 33 34 1 48 15 16 ar 49 16 17 ar 50 31 32 1 51 19 17 ar 52 17 18 1 53 5 49 1 54 5 50 1 55 6 51 1 56 8 52 1 57 9 53 1 58 10 54 1 59 12 55 1 60 14 56 1 61 18 57 1 62 18 58 1 63 20 59 1 64 28 60 1 65 28 61 1 66 29 62 1 67 31 63 1 68 32 64 1 69 33 65 1 70 34 66 1 71 35 67 1 72 37 68 1 73 41 69 1 74 41 70 1 75 42 71 1 76 43 72 1 77 44 73 1
Hi, yes, SDF or MOL is better than MOL2 for RDKit.
Hi,
EDIT: issue is resolved, I should have used sdf (mol) format instead of mol2. Sorry to waste your time.
Initial problem:
I am trying to convert NADP from mol2 to pdbqt,
mk_prepare_ligand.py -i NADP.mol2 -o NADP.pdbqt
however I get the warning:
[16:15:43] NADP: warning - O.co2 with non C.2 or S.o2 neighbor.
I guess this is related to the phosphate groups:
https://github.com/rdkit/rdkit/issues/3246 https://github.com/rdkit/rdkit/issues/1806
I would be grateful for any suggestion on how to proceed?
All the best,
Milan
NADP.mol2: