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