# Doing ligand preparation for flexible docking

**URL:** <https://gromacs.bioexcel.eu/t/doing-ligand-preparation-for-flexible-docking/8654>\
**Category:** User discussions\
**Created:** [March 20, 2024, 7:54am UTC](https://gromacs.bioexcel.eu/t/doing-ligand-preparation-for-flexible-docking/8654 "2024-03-20T07:54:42Z")\
**Posts on this page:** 7\
**Page:** 1

<div class="post-metadata">

**Author:** ![Kitkat](https://avatars.discourse-cdn.com/v4/letter/k/b487fb/32.png) [@Kitkat](https://gromacs.bioexcel.eu/u/Kitkat)\
**Post date:** [March 20, 2024, 7:54am UTC](https://gromacs.bioexcel.eu/t/doing-ligand-preparation-for-flexible-docking/8654/1 "2024-03-20T07:54:42Z")

</div>

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

> <https://github.com/Lemkul-Lab/cgenff_charmm2gmx/blob/main/cgenff_charmm2gmx_py3_nx2.py>

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

---

<div class="post-metadata">

**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [March 20, 2024, 11:20pm UTC](https://gromacs.bioexcel.eu/t/doing-ligand-preparation-for-flexible-docking/8654/2 "2024-03-20T23:20:02Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![Kitkat](https://avatars.discourse-cdn.com/v4/letter/k/b487fb/32.png) [@Kitkat](https://gromacs.bioexcel.eu/u/Kitkat)\
**Post date:** [March 21, 2024, 2:26am UTC](https://gromacs.bioexcel.eu/t/doing-ligand-preparation-for-flexible-docking/8654/3 "2024-03-21T02:26:58Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [March 21, 2024, 2:57am UTC](https://gromacs.bioexcel.eu/t/doing-ligand-preparation-for-flexible-docking/8654/4 "2024-03-21T02:57:04Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![Kitkat](https://avatars.discourse-cdn.com/v4/letter/k/b487fb/32.png) [@Kitkat](https://gromacs.bioexcel.eu/u/Kitkat)\
**Post date:** [March 21, 2024, 6:02am UTC](https://gromacs.bioexcel.eu/t/doing-ligand-preparation-for-flexible-docking/8654/5 "2024-03-21T06:02:33Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [March 21, 2024, 3:24pm UTC](https://gromacs.bioexcel.eu/t/doing-ligand-preparation-for-flexible-docking/8654/6 "2024-03-21T15:24:36Z")

</div>

in str  
`RESI 150390`  
and in mol2

```auto
 @MOLECULE
Z9.

```

You need to make same name for both.

---

<div class="post-metadata">

**Author:** ![Kitkat](https://avatars.discourse-cdn.com/v4/letter/k/b487fb/32.png) [@Kitkat](https://gromacs.bioexcel.eu/u/Kitkat)\
**Post date:** [March 22, 2024, 6:52am UTC](https://gromacs.bioexcel.eu/t/doing-ligand-preparation-for-flexible-docking/8654/7 "2024-03-22T06:52:23Z")

</div>

Thank you