Doing ligand preparation for flexible docking

User discussions
1

GROMACS version: 2021.4
GROMACS modification: No
Here post your question

Hi everyone,
I hope anyone can help me to understand the error message that I got.

I typed: python3 cgenff_charmm2gmx_py3_nx2.py Z9 z9_fix.mol2 z9_fix.str charmm36-jul2022.ff

Traceback (most recent call last):
File"/mnt/c/Users/dominikatarina/OneDrive/Desktop/MD_ubuntu22/cgenff_charmm2gmx_py3_nx2.py", line 991, in
if(float(nx.version) < 2.0):
ValueError: could not convert string to float: ‘3.2.1’

The “cgenff_charmm2gmx_py3_nx2.py” file I downloaded from

Please help me to go through this error, I am not sure what should I revise
Thank you everyone

2

The networkx version MUST be in the 1.x series. Tested version: 1.11
what is your netwekx verision?

3

Hi @scinikhil thank you for your answer.
I searched on other website and found the answer.
I try changing the line:
if(float(nx.__ version__) < 2.0):
to something like this:
if (float(nx.__ version__[0:3])<2.0):

Networkx version that I used is 3.2.1. I uninstalled it and install a new one, 1.11 version.

Now, a new error has occured:
This script has been tested with NetworkX 2.3, and 2.4 is buggy.
Please install version 2.3 for best performance:
pip uninstall networkx
pip install networkx==2.3
NOTE 1: Code tested with Python 3.5.2 and 3.7.3. Your version: 3.10.12 (main, Nov 20 2023, 15:14:05) [GCC 11.4.0]

NOTE 2: Code tested with NetworkX 2.3. Your version: 3.2.1

NOTE 3: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation:
–Version of CGenFF detected in z9_fix.str : 4.6
–Version of CGenFF detected in charmm36-jul2022.ff/forcefield.doc : 4.6

NOTE 4: To avoid duplicated parameters, do NOT select the ‘Include parameters that are already in CGenFF’ option when uploading a molecule into CGenFF.
Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (75) and top (0) are unequal
Usually this means the specified residue name does not match between str and mol2 files

What should I change so that .str and .mol2 files can be matched? And also why atoms in mol2 and top files are unequal?

Thank you

4

please attach your str file and mol2, looks like your str residue name is not match with mol2 file.

5

Below attached the .mol2 file content:
@MOLECULE
Z9
75 80 0 0 0
SMALL
GASTEIGER

@ATOM
1 N 4.0856 -0.2362 0.6651 N.pl3 1 Z9 -0.3428
2 N -2.2492 1.8910 -1.7800 N.pl3 1 Z9 -0.3428
3 N 0.4406 -2.1361 1.4854 N.ar 1 Z9 -0.2466
4 N -3.6465 -1.3767 0.4421 N.ar 1 Z9 -0.2466
5 C 2.8757 2.8418 -2.7392 C.3 1 Z9 -0.0531
6 C 3.4117 2.6880 -1.3140 C.3 1 Z9 -0.0530
7 C 1.5907 3.6714 -2.7638 C.3 1 Z9 -0.0530
8 C 4.7174 1.8900 -1.2966 C.3 1 Z9 -0.0516
9 C 0.4801 3.0016 -1.9519 C.3 1 Z9 -0.0516
10 C 5.3352 1.7660 0.0985 C.3 1 Z9 -0.0375
11 C -0.7962 3.8488 -1.9531 C.3 1 Z9 -0.0375
12 C 4.4134 1.0965 1.1135 C.3 1 Z9 0.0091
13 C -1.9473 3.1803 -1.2063 C.3 1 Z9 0.0091
14 C 2.8806 -0.8643 0.9364 C.ar 1 Z9 0.0457
15 C -2.7113 0.8105 -1.0450 C.ar 1 Z9 0.0457
16 C 2.0565 -0.4305 2.0039 C.ar 1 Z9 0.0218
17 C -3.3125 0.9960 0.2239 C.ar 1 Z9 0.0218
18 C 2.4369 -1.9588 0.1542 C.ar 1 Z9 0.0218
19 C -2.5958 -0.5110 -1.5416 C.ar 1 Z9 0.0218
20 C 0.8428 -1.0970 2.2424 C.ar 1 Z9 0.0734
21 C -3.7667 -0.1283 0.9338 C.ar 1 Z9 0.0734
22 C 1.2083 -2.5655 0.4651 C.ar 1 Z9 0.0734
23 C -3.0780 -1.5763 -0.7626 C.ar 1 Z9 0.0734
24 C 2.4464 0.6509 2.8131 C.ar 1 Z9 -0.0508
25 C -3.4534 2.2854 0.7659 C.ar 1 Z9 -0.0508
26 C 3.2138 -2.4317 -0.9178 C.ar 1 Z9 -0.0508
27 C -2.0079 -0.7541 -2.7952 C.ar 1 Z9 -0.0508
28 C 0.0487 -0.6537 3.2967 C.ar 1 Z9 -0.0357
29 C -4.3544 0.0773 2.1792 C.ar 1 Z9 -0.0357
30 C 0.7921 -3.6395 -0.3170 C.ar 1 Z9 -0.0357
31 C -2.9543 -2.8669 -1.2703 C.ar 1 Z9 -0.0357
32 C 1.6344 1.0745 3.8608 C.ar 1 Z9 -0.0610
33 C -4.0447 2.4640 2.0130 C.ar 1 Z9 -0.0610
34 C 2.7751 -3.5072 -1.6843 C.ar 1 Z9 -0.0610
35 C -1.8962 -2.0539 -3.2799 C.ar 1 Z9 -0.0610
36 C 0.4331 0.4206 4.1029 C.ar 1 Z9 -0.0597
37 C -4.4960 1.3573 2.7208 C.ar 1 Z9 -0.0597
38 C 1.5617 -4.1121 -1.3830 C.ar 1 Z9 -0.0597
39 C -2.3705 -3.1122 -2.5155 C.ar 1 Z9 -0.0597
40 H 2.6897 1.8542 -3.1784 H 1 Z9 0.0265
41 H 3.6278 3.3363 -3.3653 H 1 Z9 0.0265
42 H 3.5700 3.6742 -0.8624 H 1 Z9 0.0265
43 H 2.6773 2.1533 -0.7091 H 1 Z9 0.0265
44 H 1.2653 3.7934 -3.8038 H 1 Z9 0.0265
45 H 1.7907 4.6747 -2.3690 H 1 Z9 0.0265
46 H 4.5482 0.8950 -1.7255 H 1 Z9 0.0266
47 H 5.4483 2.3842 -1.9491 H 1 Z9 0.0266
48 H 0.2877 2.0066 -2.3686 H 1 Z9 0.0266
49 H 0.7764 2.8675 -0.9075 H 1 Z9 0.0266
50 H 5.6089 2.7635 0.4642 H 1 Z9 0.0280
51 H 6.2690 1.1955 0.0141 H 1 Z9 0.0280
52 H -1.0999 4.0341 -2.9916 H 1 Z9 0.0280
53 H -0.5911 4.8276 -1.5021 H 1 Z9 0.0280
54 H 3.5666 1.7846 1.1659 H 1 Z9 0.0461
55 H 5.0085 1.0491 2.0332 H 1 Z9 0.0461
56 H -1.5338 3.1161 -0.1936 H 1 Z9 0.0461
57 H -2.7941 3.8654 -1.3251 H 1 Z9 0.0461
58 H 4.8009 -0.7408 0.1579 H 1 Z9 0.1461
59 H -2.1453 1.7983 -2.7819 H 1 Z9 0.1461
60 H 3.4058 1.1070 2.9357 H 1 Z9 0.0625
61 H -3.3830 3.2431 0.2964 H 1 Z9 0.0625
62 H 4.1620 -1.9866 -1.2024 H 1 Z9 0.0625
63 H -1.6100 0.0353 -3.4250 H 1 Z9 0.0625
64 H -0.8969 -1.1503 3.5070 H 1 Z9 0.0639
65 H -4.7177 -0.7737 2.7525 H 1 Z9 0.0639
66 H -0.1535 -4.1323 -0.0989 H 1 Z9 0.0639
67 H -3.3168 -3.7132 -0.6896 H 1 Z9 0.0639
68 H 1.9560 1.8773 4.5181 H 1 Z9 0.0618
69 H -4.1973 3.4621 2.4134 H 1 Z9 0.0618
70 H 3.3750 -3.8688 -2.5137 H 1 Z9 0.0618
71 H -1.4379 -2.2401 -4.2463 H 1 Z9 0.0618
72 H -0.2031 0.7360 4.9247 H 1 Z9 0.0618
73 H -4.9685 1.4862 3.6901 H 1 Z9 0.0618
74 H 1.2092 -4.9515 -1.9753 H 1 Z9 0.0618
75 H -2.2859 -4.1305 -2.8832 H 1 Z9 0.0618
@BOND
1 1 12 1
2 1 14 1
3 1 58 1
4 2 13 1
5 2 15 1
6 2 59 1
7 3 20 ar
8 3 22 ar
9 4 21 ar
10 4 23 ar
11 5 6 1
12 5 7 1
13 5 40 1
14 5 41 1
15 6 8 1
16 6 42 1
17 6 43 1
18 7 9 1
19 7 44 1
20 7 45 1
21 8 10 1
22 8 46 1
23 8 47 1
24 9 11 1
25 9 48 1
26 9 49 1
27 10 12 1
28 10 50 1
29 10 51 1
30 11 13 1
31 11 52 1
32 11 53 1
33 12 54 1
34 12 55 1
35 13 56 1
36 13 57 1
37 14 16 ar
38 14 18 ar
39 15 17 ar
40 15 19 ar
41 16 20 ar
42 16 24 ar
43 17 21 ar
44 17 25 ar
45 18 22 ar
46 18 26 ar
47 19 23 ar
48 19 27 ar
49 20 28 ar
50 21 29 ar
51 22 30 ar
52 23 31 ar
53 24 32 ar
54 24 60 1
55 25 33 ar
56 25 61 1
57 26 34 ar
58 26 62 1
59 27 35 ar
60 27 63 1
61 28 36 ar
62 28 64 1
63 29 37 ar
64 29 65 1
65 30 38 ar
66 30 66 1
67 31 39 ar
68 31 67 1
69 32 36 ar
70 32 68 1
71 33 37 ar
72 33 69 1
73 34 38 ar
74 34 70 1
75 35 39 ar
76 35 71 1
77 36 72 1
78 37 73 1
79 38 74 1
80 39 75 1

Below is attached .str file content:

  • Toppar stream file generated by
  • CHARMM General Force Field (CGenFF) program version 3.0
  • For use with CGenFF version 4.6

read rtf card append

  • Topologies generated by
  • CHARMM General Force Field (CGenFF) program version 3.0

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.

RESI 150390 0.000 ! param penalty= 4.000 ; charge penalty= 2.412
!RING * 6 C12 C16 C20 C24 C28 C32
!RING * 6 N3 C10 C12 C14 C16 C18
!RING * 6 C13 C17 C21 C25 C29 C33
!RING * 6 N4 C11 C13 C15 C17 C19
!RING * 6 C14 C18 C22 C26 C30 C34
!RING * 6 C15 C19 C23 C27 C31 C35
GROUP ! CHARGE CH_PENALTY Z EL NB NBE RNG1 TYP RNG2 TYP RNG3 TYP
ATOM N1 NG311 -0.556 ! 2.412 7 N 3 3
ATOM N2 NG311 -0.556 ! 2.412 7 N 3 3
ATOM N3 NG2R60 -0.684 ! 0.000 7 N 2 3 6 1
ATOM N4 NG2R60 -0.684 ! 0.000 7 N 2 3 6 1
ATOM C1 CG321 -0.180 ! 0.000 6 C 4 4
ATOM C2 CG321 -0.180 ! 0.000 6 C 4 4
ATOM C3 CG321 -0.180 ! 0.000 6 C 4 4
ATOM C4 CG321 -0.180 ! 0.030 6 C 4 4
ATOM C5 CG321 -0.180 ! 0.030 6 C 4 4
ATOM C6 CG321 -0.198 ! 1.283 6 C 4 4
ATOM C7 CG321 -0.198 ! 1.283 6 C 4 4
ATOM C8 CG321 0.018 ! 1.265 6 C 4 4
ATOM C9 CG321 0.018 ! 1.265 6 C 4 4
ATOM C10 CG2R61 -0.002 ! 2.403 6 C 3 4 6 1
ATOM C11 CG2R61 -0.002 ! 2.403 6 C 3 4 6 1
ATOM C12 CG2R61 -0.013 ! 0.000 6 C 3 4 6 1 6 1
ATOM C13 CG2R61 -0.013 ! 0.000 6 C 3 4 6 1 6 1
ATOM C14 CG2R61 -0.013 ! 0.000 6 C 3 4 6 1 6 1
ATOM C15 CG2R61 -0.013 ! 0.000 6 C 3 4 6 1 6 1
ATOM C16 CG2R61 0.352 ! 0.000 6 C 3 4 6 1 6 1
ATOM C17 CG2R61 0.352 ! 0.000 6 C 3 4 6 1 6 1
ATOM C18 CG2R61 0.352 ! 0.000 6 C 3 4 6 1 6 1
ATOM C19 CG2R61 0.352 ! 0.000 6 C 3 4 6 1 6 1
ATOM C20 CG2R61 -0.107 ! 0.000 6 C 3 4 6 1
ATOM C21 CG2R61 -0.107 ! 0.000 6 C 3 4 6 1
ATOM C22 CG2R61 -0.107 ! 0.000 6 C 3 4 6 1
ATOM C23 CG2R61 -0.107 ! 0.000 6 C 3 4 6 1
ATOM C24 CG2R61 -0.132 ! 0.000 6 C 3 4 6 1
ATOM C25 CG2R61 -0.132 ! 0.000 6 C 3 4 6 1
ATOM C26 CG2R61 -0.132 ! 0.000 6 C 3 4 6 1
ATOM C27 CG2R61 -0.132 ! 0.000 6 C 3 4 6 1
ATOM C28 CG2R61 -0.110 ! 0.000 6 C 3 4 6 1
ATOM C29 CG2R61 -0.110 ! 0.000 6 C 3 4 6 1
ATOM C30 CG2R61 -0.110 ! 0.000 6 C 3 4 6 1
ATOM C31 CG2R61 -0.110 ! 0.000 6 C 3 4 6 1
ATOM C32 CG2R61 -0.104 ! 0.000 6 C 3 4 6 1
ATOM C33 CG2R61 -0.104 ! 0.000 6 C 3 4 6 1
ATOM C34 CG2R61 -0.104 ! 0.000 6 C 3 4 6 1
ATOM C35 CG2R61 -0.104 ! 0.000 6 C 3 4 6 1
ATOM H1 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H2 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H3 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H4 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H5 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H6 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H7 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H8 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H9 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H10 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H11 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H12 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H13 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H14 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H15 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H16 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H17 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H18 HGA2 0.090 ! 0.000 1 H 1 1
ATOM H19 HGPAM1 0.370 ! 0.000 1 H 1 1
ATOM H20 HGPAM1 0.370 ! 0.000 1 H 1 1
ATOM H21 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H22 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H23 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H24 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H25 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H26 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H27 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H28 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H29 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H30 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H31 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H32 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H33 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H34 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H35 HGR61 0.115 ! 0.000 1 H 1 1
ATOM H36 HGR61 0.115 ! 0.000 1 H 1 1
! TYP INR
BOND N1 C8 ! 1 0
BOND N1 C10 ! 1 0
BOND N1 H19 ! 1 0
BOND N2 C9 ! 1 0
BOND N2 C11 ! 1 0
BOND N2 H20 ! 1 0
BOND N3 C16 ! 2 1
BOND N3 C18 ! 1 1
BOND N4 C17 ! 2 1
BOND N4 C19 ! 1 1
BOND C1 C2 ! 1 0
BOND C1 C3 ! 1 0
BOND C1 H1 ! 1 0
BOND C1 H2 ! 1 0
BOND C2 C4 ! 1 0
BOND C2 H3 ! 1 0
BOND C2 H4 ! 1 0
BOND C3 C5 ! 1 0
BOND C3 H5 ! 1 0
BOND C3 H6 ! 1 0
BOND C4 C6 ! 1 0
BOND C4 H7 ! 1 0
BOND C4 H8 ! 1 0
BOND C5 C7 ! 1 0
BOND C5 H9 ! 1 0
BOND C5 H10 ! 1 0
BOND C6 C8 ! 1 0
BOND C6 H11 ! 1 0
BOND C6 H12 ! 1 0
BOND C7 C9 ! 1 0
BOND C7 H13 ! 1 0
BOND C7 H14 ! 1 0
BOND C8 H15 ! 1 0
BOND C8 H16 ! 1 0
BOND C9 H17 ! 1 0
BOND C9 H18 ! 1 0
BOND C10 C12 ! 2 1
BOND C10 C14 ! 1 1
BOND C11 C13 ! 2 1
BOND C11 C15 ! 1 1
BOND C12 C16 ! 1 1
BOND C12 C20 ! 1 1
BOND C13 C17 ! 1 1
BOND C13 C21 ! 1 1
BOND C14 C18 ! 2 1
BOND C14 C22 ! 1 1
BOND C15 C19 ! 2 1
BOND C15 C23 ! 1 1
BOND C16 C24 ! 1 1
BOND C17 C25 ! 1 1
BOND C18 C26 ! 1 1
BOND C19 C27 ! 1 1
BOND C20 C28 ! 2 1
BOND C20 H21 ! 1 0
BOND C21 C29 ! 2 1
BOND C21 H22 ! 1 0
BOND C22 C30 ! 2 1
BOND C22 H23 ! 1 0
BOND C23 C31 ! 2 1
BOND C23 H24 ! 1 0
BOND C24 C32 ! 2 1
BOND C24 H25 ! 1 0
BOND C25 C33 ! 2 1
BOND C25 H26 ! 1 0
BOND C26 C34 ! 2 1
BOND C26 H27 ! 1 0
BOND C27 C35 ! 2 1
BOND C27 H28 ! 1 0
BOND C28 C32 ! 1 1
BOND C28 H29 ! 1 0
BOND C29 C33 ! 1 1
BOND C29 H30 ! 1 0
BOND C30 C34 ! 1 1
BOND C30 H31 ! 1 0
BOND C31 C35 ! 1 1
BOND C31 H32 ! 1 0
BOND C32 H33 ! 1 0
BOND C33 H34 ! 1 0
BOND C34 H35 ! 1 0
BOND C35 H36 ! 1 0

END

read param card flex append

  • Parameters generated by analogy by
  • CHARMM General Force Field (CGenFF) program version 3.0

! 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
CG321 CG321 NG311 CG2R61 0.8000 1 180.00 ! 150390 , from CG321 CG321 NG311 CG2R64, penalty= 4
CG321 CG321 NG311 CG2R61 1.1000 3 0.00 ! 150390 , from CG321 CG321 NG311 CG2R64, penalty= 4

IMPROPERS

END
RETURN

6

in str
RESI 150390
and in mol2

 @MOLECULE
Z9.

You need to make same name for both.

7

Thank you