# cGenFF Ligand topology **URL:** \ **Category:** User discussions\ **Tags:** forcefield, topology\ **Created:** [March 13, 2025, 2:12am UTC](https://gromacs.bioexcel.eu/t/cgenff-ligand-topology/11732 "2025-03-13T02:12:42Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![AndreaMx](https://avatars.discourse-cdn.com/v4/letter/a/ee7513/32.png) [@AndreaMx](https://gromacs.bioexcel.eu/u/AndreaMx)\ **Post date:** [March 13, 2025, 2:12am UTC](https://gromacs.bioexcel.eu/t/cgenff-ligand-topology/11732/1 "2025-03-13T02:12:42Z")
GROMACS version: 2023 GROMACS modification: No Hi I am new in this field, I am doing the protein ligand complex tutorial from the website but applied to my protein and ligand of interest . I am in the step of generating topology of ligand in cGenFF for generate the .str file but when I upload my .mol2 file , I have some issues : First the param penalty and charge penalty don´t show any value, then in the results my .str file doesn´t have any information, and when I select convert to Gromacs, a warning says that my mol2 file is imposible to convert. Mi str file says the next: - Toppar stream file generated by - CHARMM General Force Field (CGenFF) program version 4.0 - For use with CGenFF version 4.6 - read rtf card append - Topologies generated by - CHARMM General Force Field (CGenFF) program version 4.0 - 36 1 ! “penalty” is the highest penalty score of the associated parameters. ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. END read param card flex append - Parameters generated by analogy by - CHARMM General Force Field (CGenFF) program version 4.0 - ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. BONDS ANGLES DIHEDRALS IMPROPERS END RETURN Also I add my mol2 file: @MOLECULE BRAD 93 97 0 0 0 SMALL GASTEIGER @ATOM 1 C 21.6690 3.5200 -6.7160 C.2 5 BRAD 0.2704 2 O 21.8190 2.7990 -5.7230 O.2 5 BRAD -0.2678 3 N 20.7140 3.4270 -7.6790 N.am 6 BRAD -0.2765 4 H 20.6840 4.0590 -8.4330 H 6 BRAD 0.1551 5 CA 22.6820 4.6960 -6.9790 C.2 5 BRAD 0.1402 6 N 24.0360 4.4940 -6.8070 N.am 5 BRAD -0.2731 7 C 24.7010 3.6090 -7.5720 C.2 4 BRAD 0.2467 8 O 24.3290 2.5380 -8.0570 O.2 4 BRAD -0.2729 9 H 24.5200 5.0020 -6.1160 H 5 BRAD 0.1556 10 CA 26.1280 3.9350 -7.7970 C.3 4 BRAD 0.1763 11 N 27.5580 4.2930 -8.0130 N.am 4 BRAD -0.2919 12 C 28.1980 4.9710 -7.0500 C.2 3 BRAD 0.2625 13 O 29.3510 5.4040 -7.1460 O.2 3 BRAD -0.2685 14 H 28.0220 4.0380 -8.8430 H 4 BRAD 0.1502 15 CA 27.5130 5.1330 -5.7480 C.ar 3 BRAD 0.1202 16 CB 27.7290 4.3240 -4.5830 C.ar 3 BRAD 0.0238 17 CG 27.2300 4.7590 -3.2040 C.ar 3 BRAD 0.0207 18 CD 26.7470 5.9920 -3.9560 C.ar 3 BRAD 0.0832 19 N 26.8770 6.2870 -5.2790 N.ar 3 BRAD -0.2676 20 C 26.4850 7.3770 -6.0390 C.2 2 BRAD 0.2811 21 O 26.7080 7.6010 -7.2260 O.2 2 BRAD -0.2650 22 CA 25.6360 8.3670 -5.2980 C.ar 2 BRAD 0.1232 23 CB 24.2010 8.3000 -5.2350 C.ar 2 BRAD 0.0240 24 CG 23.3200 9.5500 -5.2420 C.ar 2 BRAD 0.0207 25 CD 24.6560 10.2790 -5.2810 C.ar 2 BRAD 0.0829 26 N 25.9060 9.7460 -5.2720 N.ar 2 BRAD -0.2702 27 C 27.1300 10.3790 -5.4240 C.2 1 BRAD 0.2681 28 O 27.2400 11.5130 -5.9010 O.2 1 BRAD -0.2691 29 CA 28.3010 9.7210 -4.7620 C.3 1 BRAD 0.1964 30 CB 28.7360 10.2490 -3.5100 C.1 1 BRAD -0.0629 31 CG 29.0500 10.8020 -2.1130 C.1 1 BRAD -0.0462 32 CD 29.3380 11.4310 -0.7410 C.3 1 BRAD 0.2518 33 NE 29.6300 12.0010 0.5720 N.pl3 1 BRAD -0.2510 34 CZ 28.6070 12.0340 1.4190 C.cat 1 BRAD 0.3777 35 NH1 28.8140 12.5010 2.5640 N.pl3 1 BRAD -0.1297 36 NH2 27.2900 11.5810 1.1190 N.pl3 1 BRAD -0.2892 37 HH1 28.0810 12.5420 3.2200 H 1 BRAD 0.3062 38 1HH2 26.5820 11.6390 1.8020 H 1 BRAD 0.2546 39 2HH2 27.0860 11.2110 0.2300 H 1 BRAD 0.2546 40 HE 30.5230 12.3370 0.8120 H 1 BRAD 0.2597 41 N 29.3200 9.1450 -5.5860 N.3 1 BRAD -0.3046 42 H1 28.9190 8.3930 -6.1460 H 1 BRAD 0.1201 43 H2 30.0640 8.7700 -4.9950 H 1 BRAD 0.1201 44 CB 22.1800 5.9920 -7.3210 C.1 5 BRAD -0.0826 45 CG 21.7110 7.2860 -7.6800 C.2 5 BRAD 0.0351 46 CD1 20.5010 7.7470 -7.1670 C.2 5 BRAD 0.0034 47 CE1 20.0320 9.0100 -7.5210 C.2 5 BRAD -0.0208 48 CZ 20.7750 9.8090 -8.3880 C.3 5 BRAD 0.0520 49 CE2 21.9860 9.3460 -8.8990 C.2 5 BRAD -0.0208 50 CD2 22.4550 8.0830 -8.5450 C.2 5 BRAD 0.0034 51 CA 19.7920 2.4160 -7.5620 C.2 6 BRAD 0.1147 52 C 18.9140 2.3230 -6.2750 C.2 6 BRAD 0.2767 53 O 19.0190 1.3950 -5.4680 O.2 6 BRAD -0.2655 54 N 18.0490 3.4160 -6.1210 N.ar 7 BRAD -0.2680 55 CA 17.0190 3.6100 -5.1810 C.ar 7 BRAD 0.1205 56 CD 18.0910 4.6430 -6.7140 C.ar 7 BRAD 0.0832 57 CB 16.6450 4.9900 -5.3650 C.ar 7 BRAD 0.0238 58 CG 17.2810 5.8970 -6.4170 C.ar 7 BRAD 0.0207 59 C 16.1810 2.6150 -4.4280 C.2 7 BRAD 0.2663 60 O 16.5570 1.4580 -4.2460 O.2 7 BRAD -0.2682 61 N 15.0220 3.1660 -4.0070 N.am 8 BRAD -0.2697 62 H 15.0280 3.9250 -3.3800 H 8 BRAD 0.1559 63 CA 13.8380 2.6460 -4.4670 C.2 8 BRAD 0.1402 64 C 12.5140 3.4410 -4.2170 C.2 8 BRAD 0.2710 65 O 12.2650 4.4510 -4.8790 O.2 8 BRAD -0.2678 66 N 11.7560 2.8510 -3.2660 N.am 9 BRAD -0.2674 67 H 12.0220 1.9670 -2.9220 H 9 BRAD 0.1560 68 CA 10.6280 3.4470 -2.7640 C.2 9 BRAD 0.1698 69 C 9.1450 3.2870 -3.2410 C.2 9 BRAD 0.3598 70 O 8.3630 2.6410 -2.4610 O.2 9 BRAD -0.2430 71 OXT 8.9080 3.5910 -4.4620 O.3 9 BRAD -0.4758 72 HXT 9.5590 3.4360 -5.1190 H 9 BRAD 0.2955 73 CB 10.8550 4.3810 -1.6830 C.1 9 BRAD -0.0395 74 CG 11.1070 5.3960 -0.5200 C.1 9 BRAD -0.0419 75 CD 11.3410 6.4380 0.6240 C.3 9 BRAD 0.2521 76 NE 11.5010 7.4440 1.6900 N.pl3 9 BRAD -0.2510 77 CZ 10.9570 8.6380 1.4820 C.cat 9 BRAD 0.3777 78 NH1 10.3370 8.9720 0.4430 N.pl3 9 BRAD -0.1297 79 NH2 11.0870 9.6140 2.5130 N.pl3 9 BRAD -0.2892 80 HH1 10.2260 8.3270 -0.2920 H 9 BRAD 0.3062 81 1HH2 11.5660 9.3920 3.3440 H 9 BRAD 0.2546 82 2HH2 10.6990 10.5110 2.3930 H 9 BRAD 0.2546 83 HE 11.9890 7.2390 2.5200 H 9 BRAD 0.2597 84 CB 13.8370 1.4920 -5.3210 C.1 8 BRAD -0.0865 85 CG 13.9020 0.3680 -6.1930 C.2 8 BRAD 0.0179 86 CD1 13.0310 -0.7040 -6.0050 C.3 8 BRAD 0.0601 87 CE1 13.0810 -1.8020 -6.8610 C.2 8 BRAD -0.0208 88 CZ 14.0050 -1.8280 -7.9030 C.2 8 BRAD -0.0042 89 CE2 14.8750 -0.7570 -8.0900 C.2 8 BRAD -0.0000 90 CD2 14.8240 0.3430 -7.2350 C.2 8 BRAD 0.0037 91 CB 20.0700 1.1670 -8.2690 C.3 6 BRAD 0.1833 92 OG 20.3690 0.0210 -8.9940 O.3 6 BRAD -0.3761 93 H 19.5550 -0.4800 -9.1590 H 6 BRAD 0.2110 @BOND 1 93 92 1 2 92 91 1 3 49 50 2 4 49 48 1 5 14 11 1 6 50 45 1 7 4 3 1 8 48 47 1 9 91 51 1 10 89 88 1 11 89 90 2 12 8 7 2 13 11 10 1 14 11 12 am 15 88 87 2 16 10 7 1 17 45 44 2 18 45 46 1 19 3 51 2 20 3 1 am 21 7 6 am 22 51 52 1 23 47 46 2 24 44 5 2 25 90 85 1 26 21 20 2 27 13 12 2 28 12 15 1 29 5 6 1 30 5 1 1 31 87 86 1 32 6 9 1 33 1 2 2 34 56 58 ar 35 56 54 ar 36 58 57 ar 37 52 54 am 38 52 53 2 39 85 86 1 40 85 84 2 41 42 41 1 42 54 55 ar 43 20 22 1 44 20 19 am 45 28 27 2 46 15 19 ar 47 15 16 ar 48 41 43 1 49 41 29 1 50 27 26 am 51 27 29 1 52 57 55 ar 53 84 63 2 54 22 26 ar 55 22 23 ar 56 25 26 ar 57 25 24 ar 58 19 18 ar 59 24 23 ar 60 55 59 1 61 72 71 1 62 65 64 2 63 29 30 1 64 16 17 ar 65 63 64 1 66 63 61 1 67 71 69 1 68 59 60 2 69 59 61 am 70 64 66 am 71 61 62 1 72 18 17 ar 73 30 31 3 74 66 67 1 75 66 68 2 76 69 68 1 77 69 70 2 78 68 73 1 79 31 32 1 80 73 74 3 81 32 33 1 82 74 75 1 83 80 78 1 84 39 36 1 85 78 77 1 86 33 40 1 87 33 34 1 88 75 76 1 89 36 34 2 90 36 38 1 91 34 35 1 92 77 76 1 93 77 79 2 94 76 83 1 95 82 79 1 96 79 81 1 97 35 37 1 (This is a peptide, bradykinin, the result from docking with Autodock Vina) and the others files that the results from cGenFF give me like BK\_dock1.err: CHARMM General Force Field (CGenFF) program version 4.0 released June 2024 Copyright (C) 2020 SilcBio LLC and University of Maryland, School of Pharmacy. All Rights Reserved. Licensed to: cgenff server serverncgenff License expires: Tue Dec 31 00:00:00 2030 readpar debug: read 683 bonds, 2501 angles, 7460 dihedrals, 203 impropers and 375437 characters worth of comments. readmol2 warning: renaming non-unique atom 1HH2 to 1HH1 . readmol2 warning: renaming non-unique atom 2HH2 to 2HH1 . readmol2 warning: renaming non-unique atom CA to CA1 . readmol2 warning: renaming non-unique atom CA to CA2 . readmol2 warning: renaming non-unique atom CA to CA3 . readmol2 warning: renaming non-unique atom CA to CA4 . readmol2 warning: renaming non-unique atom CA to CA5 . readmol2 warning: renaming non-unique atom CA to CA6 . readmol2 warning: renaming non-unique atom CA to CA7 . readmol2 warning: renaming non-unique atom CA to CA8 . readmol2 warning: renaming non-unique atom CA to CA9 . readmol2 warning: renaming non-unique atom CB to CB1 . readmol2 warning: renaming non-unique atom CB to CB2 . readmol2 warning: renaming non-unique atom CB to CB3 . readmol2 warning: renaming non-unique atom CB to CB4 . readmol2 warning: renaming non-unique atom CB to CB5 . readmol2 warning: renaming non-unique atom CB to CB6 . readmol2 warning: renaming non-unique atom CB to CB7 . readmol2 warning: renaming non-unique atom CB to CB8 . readmol2 warning: renaming non-unique atom CD to CD3 . readmol2 warning: renaming non-unique atom CD to CD4 . readmol2 warning: renaming non-unique atom CD to CD5 . readmol2 warning: renaming non-unique atom CD to CD6 . readmol2 warning: renaming non-unique atom CD to CD7 . readmol2 warning: renaming non-unique atom CD1 to CD8 . readmol2 warning: renaming non-unique atom CD2 to CD9 . readmol2 warning: renaming non-unique atom CE1 to CE3 . readmol2 warning: renaming non-unique atom CE2 to CE4 . readmol2 warning: renaming non-unique atom CG to CG1 . readmol2 warning: renaming non-unique atom CG to CG2 . readmol2 warning: renaming non-unique atom CG to CG3 . readmol2 warning: renaming non-unique atom CG to CG4 . readmol2 warning: renaming non-unique atom CG to CG5 . readmol2 warning: renaming non-unique atom CG to CG6 . readmol2 warning: renaming non-unique atom CG to CG7 . readmol2 warning: renaming non-unique atom CZ to CZ1 . readmol2 warning: renaming non-unique atom CZ to CZ2 . readmol2 warning: renaming non-unique atom CZ to CZ3 . readmol2 warning: renaming non-unique atom CZ to CZ4 . readmol2 warning: renaming non-unique atom HE to HE1 . readmol2 warning: renaming non-unique atom HE to HE2 . readmol2 warning: renaming non-unique atom HH1 to HH2 . readmol2 warning: renaming non-unique atom NE to NE1 . readmol2 warning: renaming non-unique atom NE to NE2 . readmol2 warning: renaming non-unique atom NH1 to NH3 . readmol2 warning: renaming non-unique atom NH2 to NH4 . readmol2 warning: renaming non-unique atom C to C1 . readmol2 warning: renaming non-unique atom C to C2 . readmol2 warning: renaming non-unique atom C to C3 . readmol2 warning: renaming non-unique atom C to C4 . readmol2 warning: renaming non-unique atom C to C5 . readmol2 warning: renaming non-unique atom C to C6 . readmol2 warning: renaming non-unique atom C to C7 . readmol2 warning: renaming non-unique atom C to C8 . readmol2 warning: renaming non-unique atom C to C9 . readmol2 warning: renaming non-unique atom H to H3 . readmol2 warning: renaming non-unique atom H to H4 . readmol2 warning: renaming non-unique atom H to H5 . readmol2 warning: renaming non-unique atom H to H6 . readmol2 warning: renaming non-unique atom H to H7 . readmol2 warning: renaming non-unique atom H to H8 . readmol2 warning: renaming non-unique atom N to N1 . readmol2 warning: renaming non-unique atom N to N2 . readmol2 warning: renaming non-unique atom N to N3 . readmol2 warning: renaming non-unique atom N to N4 . readmol2 warning: renaming non-unique atom N to N5 . readmol2 warning: renaming non-unique atom N to N6 . readmol2 warning: renaming non-unique atom N to N7 . readmol2 warning: renaming non-unique atom N to N8 . readmol2 warning: renaming non-unique atom N to N9 . readmol2 warning: renaming non-unique atom O to O1 . readmol2 warning: renaming non-unique atom O to O2 . readmol2 warning: renaming non-unique atom O to O3 . readmol2 warning: renaming non-unique atom O to O4 . readmol2 warning: renaming non-unique atom O to O5 . readmol2 warning: renaming non-unique atom O to O6 . readmol2 warning: renaming non-unique atom O to O7 . readmol2 warning: renaming non-unique atom O to O8 . readmol2 warning: renaming non-unique atom O to O9 . Now processing molecule BRAD … ringper debug: stored 6-membered ring in stage 1. ringper debug: stored 5-membered ring in stage 1. ringper debug: stored 6-membered ring in stage 1. ringper debug: stored 5-membered ring in stage 1. ringper debug: stored 5-membered ring in stage 1. resonance warning: unfulfilled valence in aromatic subgraph; skipped molecule Thank you! I hope you can help me