# Correcting non integral charge on ligand
**URL:** https://gromacs.bioexcel.eu/t/correcting-non-integral-charge-on-ligand/7652
**Category:** User discussions
**Created:** [November 15, 2023, 3:39pm UTC](https://gromacs.bioexcel.eu/t/correcting-non-integral-charge-on-ligand/7652 "2023-11-15T15:39:20Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@KavyashreeM](https://gromacs.bioexcel.eu/u/KavyashreeM)
#### Post date: [November 15, 2023, 3:39pm UTC](https://gromacs.bioexcel.eu/t/correcting-non-integral-charge-on-ligand/7652/1 "2023-11-15T15:39:21Z")
GROMACS version: 2020.4
GROMACS modification: No
Dear all,
I was trying to simulate a protein ligand complex in Gromacs 2020.4, using OPLSAAff. the parameters for ligand was generated using the server LigParGen. The total charge on the ligand sums up to 0.0002, how to deal with this?
I checked for any floating point error according to this [https://manual.gromacs.org/current/user-guide/floating-point.html](https://manual.gromacs.org/current/user-guide/floating-point.html), but couldnt find any such charges.
I saw the similar question posted earlier, which ended up saying “topology needs to be corrected”, It would be helpful if it can be elaborated.
Thanks
Kavya
---
### Author:  [@KavyashreeM](https://gromacs.bioexcel.eu/u/KavyashreeM)
#### Post date: [November 15, 2023, 4:12pm UTC](https://gromacs.bioexcel.eu/t/correcting-non-integral-charge-on-ligand/7652/2 "2023-11-15T16:12:42Z")
The second point I made regarding floating point error may be incorrect. sorry.
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [November 15, 2023, 4:24pm UTC](https://gromacs.bioexcel.eu/t/correcting-non-integral-charge-on-ligand/7652/3 "2023-11-15T16:24:39Z")
LigParGen frequently has rounding issues internally and does not generate correct charges. Given the small error, you can likely subtract 0.0002 from one atom’s charge and the topology will still be reasonable. Without more detail, it is not possible to make a specific recommendation. But the topology is not correct if it has a non-integer charge.
---
### Author:  [@KavyashreeM](https://gromacs.bioexcel.eu/u/KavyashreeM)
#### Post date: [November 16, 2023, 7:19am UTC](https://gromacs.bioexcel.eu/t/correcting-non-integral-charge-on-ligand/7652/4 "2023-11-16T07:19:55Z")
Thank you Justin. I am attaching a part of the topology file herewith. How to identify the error in the topology?
Thank you
Kavya
;
; GENERATED BY LigParGen Server
; Jorgensen Lab @ Yale University
;
[atomtypes]
opls\_814 C814 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_874 H874 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_842 H842 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_864 H864 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_815 C815 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_805 C805 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_817 C817 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls\_843 H843 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_836 H836 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_834 H834 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_810 C810 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_827 C827 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_825 C825 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_860 H860 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_851 H851 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_873 H873 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_875 H875 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_802 C802 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_828 C828 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_818 O818 15.9990 0.000 A 2.96000E-01 8.78640E-01
opls\_861 H861 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_801 C801 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_806 C806 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_844 H844 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_803 C803 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_838 H838 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_867 H867 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_830 H830 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_804 C804 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_848 H848 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_821 C821 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_837 H837 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_824 C824 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_852 H852 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_831 H831 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_822 C822 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_853 H853 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_856 H856 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_832 H832 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_800 C800 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_858 H858 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_846 H846 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_829 C829 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_862 H862 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_811 C811 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_866 H866 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_833 H833 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_819 C819 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_869 H869 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_820 C820 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_868 H868 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_835 H835 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_841 H841 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_871 H871 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_876 H876 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_816 C816 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_855 H855 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_839 H839 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_857 H857 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_870 H870 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_812 C812 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_808 C808 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_850 H850 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_840 H840 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_877 H877 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_809 C809 12.0110 0.000 A 3.45000E-01 3.47272E-01
opls\_849 H849 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_813 C813 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_859 H859 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_847 H847 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_826 C826 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_863 H863 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_823 C823 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_845 H845 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_854 H854 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_872 H872 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls\_807 C807 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls\_865 H865 1.0080 0.000 A 2.50000E-01 1.25520E-01
[moleculetype]
; Name nrexcl
UNK 3
[atoms]
; nr type resnr residue atom cgnr charge mass
1 opls\_800 1 UNK C00 1 -0.2357 12.0110
2 opls\_801 1 UNK C01 1 -0.1377 12.0110
3 opls\_802 1 UNK C02 1 -0.1881 12.0110
4 opls\_803 1 UNK C03 1 -0.1945 12.0110
5 opls\_804 1 UNK C04 1 -0.1298 12.0110
6 opls\_805 1 UNK C05 1 -0.1782 12.0110
7 opls\_806 1 UNK C06 1 -0.1918 12.0110
8 opls\_807 1 UNK C07 1 -0.0232 12.0110
9 opls\_808 1 UNK C08 1 -0.2533 12.0110
10 opls\_809 1 UNK C09 1 -0.3197 12.0110
11 opls\_810 1 UNK C0A 1 -0.1187 12.0110
12 opls\_811 1 UNK C0B 1 -0.1833 12.0110
13 opls\_812 1 UNK C0C 1 -0.101 12.0110
14 opls\_813 1 UNK C0D 1 -0.0631 12.0110
15 opls\_814 1 UNK C0E 1 -0.2636 12.0110
16 opls\_815 1 UNK C0F 1 -0.181 12.0110
17 opls\_816 1 UNK C0G 1 -0.2342 12.0110
18 opls\_817 1 UNK C0H 1 0.3772 12.0110
19 opls\_818 1 UNK O0I 1 -0.4868 15.9990
20 opls\_819 1 UNK C0J 1 -0.1236 12.0110
21 opls\_820 1 UNK C0K 1 -0.2122 12.0110
22 opls\_821 1 UNK C0M 1 -0.221 12.0110
23 opls\_822 1 UNK C0N 1 -0.0957 12.0110
24 opls\_823 1 UNK C0O 1 -0.1978 12.0110
25 opls\_824 1 UNK C0P 1 -0.1805 12.0110
26 opls\_825 1 UNK C0Q 1 -0.0664 12.0110
27 opls\_826 1 UNK C0R 1 -0.2555 12.0110
28 opls\_827 1 UNK C0S 1 -0.0348 12.0110
29 opls\_828 1 UNK C0T 1 -0.1189 12.0110
30 opls\_829 1 UNK C0U 1 -0.2303 12.0110
31 opls\_830 1 UNK H0V 1 0.0833 1.0080
32 opls\_831 1 UNK H0W 1 0.0833 1.0080
33 opls\_832 1 UNK H0X 2 0.0833 1.0080
34 opls\_833 1 UNK H0Y 2 0.1058 1.0080
35 opls\_834 1 UNK H0Z 2 0.106 1.0080
36 opls\_835 1 UNK H10 2 0.106 1.0080
37 opls\_836 1 UNK H11 2 0.0986 1.0080
38 opls\_837 1 UNK H12 2 0.0986 1.0080
39 opls\_838 1 UNK H13 2 0.1 1.0080
40 opls\_839 1 UNK H14 2 0.1057 1.0080
41 opls\_840 1 UNK H15 2 0.1057 1.0080
42 opls\_841 1 UNK H16 2 0.1008 1.0080
43 opls\_842 1 UNK H17 2 0.1008 1.0080
44 opls\_843 1 UNK H18 2 0.0871 1.0080
45 opls\_844 1 UNK H19 2 0.0871 1.0080
46 opls\_845 1 UNK H1A 2 0.0871 1.0080
47 opls\_846 1 UNK H1B 2 0.1973 1.0080
48 opls\_847 1 UNK H1C 2 0.067 1.0080
49 opls\_848 1 UNK H1D 2 0.067 1.0080
50 opls\_849 1 UNK H1E 2 0.1097 1.0080
51 opls\_850 1 UNK H1F 2 0.1097 1.0080
52 opls\_851 1 UNK H1G 2 0.1094 1.0080
53 opls\_852 1 UNK H1H 2 0.0915 1.0080
54 opls\_853 1 UNK H1I 2 0.0915 1.0080
55 opls\_854 1 UNK H1J 2 0.0915 1.0080
56 opls\_855 1 UNK H1K 2 0.1103 1.0080
57 opls\_856 1 UNK H1M 2 0.1103 1.0080
58 opls\_857 1 UNK H1N 2 0.1377 1.0080
59 opls\_858 1 UNK H1O 2 0.1377 1.0080
60 opls\_859 1 UNK H1P 2 0.0967 1.0080
61 opls\_860 1 UNK H1Q 2 0.0967 1.0080
62 opls\_861 1 UNK H1R 2 0.0967 1.0080
63 opls\_862 1 UNK H1S 2 0.094 1.0080
64 opls\_863 1 UNK H1T 2 0.094 1.0080
65 opls\_864 1 UNK H1U 2 0.094 1.0080
66 opls\_865 1 UNK H1V 3 0.0984 1.0080
67 opls\_866 1 UNK H1W 3 0.1101 1.0080
68 opls\_867 1 UNK H1X 3 0.1101 1.0080
69 opls\_868 1 UNK H1Y 3 0.1191 1.0080
70 opls\_869 1 UNK H1Z 3 0.1191 1.0080
71 opls\_870 1 UNK H20 3 0.0953 1.0080
72 opls\_871 1 UNK H21 3 0.0953 1.0080
73 opls\_872 1 UNK H22 3 0.0953 1.0080
74 opls\_873 1 UNK H23 3 0.09 1.0080
75 opls\_874 1 UNK H24 3 0.1138 1.0080
76 opls\_875 1 UNK H25 3 0.085 1.0080
77 opls\_876 1 UNK H26 3 0.085 1.0080
78 opls\_877 1 UNK H27 3 0.085 1.0080
[bonds]
2 1 1 0.1529 224262.400
3 2 1 0.1529 224262.400
4 3 1 0.1529 224262.400
5 4 1 0.1529 224262.400
6 5 1 0.1529 224262.400
7 6 1 0.1529 224262.400
8 7 1 0.1529 224262.400
9 8 1 0.1529 224262.400
10 8 1 0.1510 234304.000
11 10 1 0.1510 234304.000
12 11 1 0.1529 224262.400
13 12 1 0.1529 224262.400
14 13 1 0.1529 224262.400
15 14 1 0.1529 224262.400
16 14 1 0.1529 224262.400
17 16 1 0.1529 224262.400
18 17 1 0.1522 265265.600
19 18 1 0.1229 476976.000
20 18 1 0.1522 265265.600
21 20 1 0.1529 224262.400
22 20 1 0.1529 224262.400
23 14 1 0.1529 224262.400
24 23 1 0.1529 224262.400
25 24 1 0.1529 224262.400
26 8 1 0.1529 224262.400
27 26 1 0.1529 224262.400
28 5 1 0.1529 224262.400
29 2 1 0.1529 224262.400
30 29 1 0.1529 224262.400
31 1 1 0.1090 284512.000
32 1 1 0.1090 284512.000
33 1 1 0.1090 284512.000
34 2 1 0.1090 284512.000
35 3 1 0.1090 284512.000
36 3 1 0.1090 284512.000
37 4 1 0.1090 284512.000
38 4 1 0.1090 284512.000
39 5 1 0.1090 284512.000
40 6 1 0.1090 284512.000
41 6 1 0.1090 284512.000
42 7 1 0.1090 284512.000
43 7 1 0.1090 284512.000
44 9 1 0.1090 284512.000
45 9 1 0.1090 284512.000
46 9 1 0.1090 284512.000
47 10 1 0.1088 284512.000
48 11 1 0.1090 284512.000
49 11 1 0.1090 284512.000
50 12 1 0.1090 284512.000
51 12 1 0.1090 284512.000
52 13 1 0.1090 284512.000
53 15 1 0.1090 284512.000
54 15 1 0.1090 284512.000
55 15 1 0.1090 284512.000
56 16 1 0.1090 284512.000
57 16 1 0.1090 284512.000
58 17 1 0.1090 284512.000
59 17 1 0.1090 284512.000
60 21 1 0.1090 284512.000
61 21 1 0.1090 284512.000
62 21 1 0.1090 284512.000
63 22 1 0.1090 284512.000
64 22 1 0.1090 284512.000
65 22 1 0.1090 284512.000
66 23 1 0.1090 284512.000
67 24 1 0.1090 284512.000
68 24 1 0.1090 284512.000
69 25 1 0.1090 284512.000
70 25 1 0.1090 284512.000
71 27 1 0.1090 284512.000
72 27 1 0.1090 284512.000
73 27 1 0.1090 284512.000
74 28 1 0.1090 284512.000
75 29 1 0.1090 284512.000
76 30 1 0.1090 284512.000
77 30 1 0.1090 284512.000
78 30 1 0.1090 284512.000
28 10 1 0.1510 234304.000
26 13 1 0.1529 224262.400
23 20 1 0.1529 224262.400
26 25 1 0.1529 224262.400
29 28 1 0.1529 224262.400
[angles]
; ai aj ak funct c0 c1 c2 c3
1 2 3 1 112.700 488.273
2 3 4 1 112.700 488.273
3 4 5 1 112.700 488.273
4 5 6 1 112.700 488.273
5 6 7 1 112.700 488.273
6 7 8 1 112.700 488.273
7 8 9 1 112.700 488.273
7 8 10 1 112.700 488.273
8 10 11 1 114.300 292.880
10 11 12 1 112.700 488.273
11 12 13 1 112.700 488.273
12 13 14 1 112.700 488.273
13 14 15 1 112.700 488.273
13 14 16 1 112.700 488.273
14 16 17 1 112.700 488.273
16 17 18 1 111.100 527.184
17 18 19 1 120.400 669.440
17 18 20 1 116.000 585.760
18 20 21 1 111.100 527.184
18 20 22 1 111.100 527.184
13 14 23 1 112.700 488.273
14 23 24 1 112.700 488.273
23 24 25 1 112.700 488.273
7 8 26 1 112.700 488.273
8 26 27 1 112.700 488.273
4 5 28 1 112.700 488.273
1 2 29 1 112.700 488.273
2 29 30 1 112.700 488.273
2 1 31 1 110.700 313.800
2 1 32 1 110.700 313.800
2 1 33 1 110.700 313.800
1 2 34 1 110.700 313.800
2 3 35 1 110.700 313.800
2 3 36 1 110.700 313.800
3 4 37 1 110.700 313.800
3 4 38 1 110.700 313.800
4 5 39 1 110.700 313.800
5 6 40 1 110.700 313.800
5 6 41 1 110.700 313.800
6 7 42 1 110.700 313.800
6 7 43 1 110.700 313.800
8 9 44 1 110.700 313.800
8 9 45 1 110.700 313.800
8 9 46 1 110.700 313.800
8 10 47 1 114.300 292.880
10 11 48 1 110.700 313.800
10 11 49 1 110.700 313.800
11 12 50 1 110.700 313.800
11 12 51 1 110.700 313.800
12 13 52 1 110.700 313.800
14 15 53 1 110.700 313.800
14 15 54 1 110.700 313.800
14 15 55 1 110.700 313.800
14 16 56 1 110.700 313.800
14 16 57 1 110.700 313.800
16 17 58 1 110.700 313.800
16 17 59 1 110.700 313.800
20 21 60 1 110.700 313.800
20 21 61 1 110.700 313.800
20 21 62 1 110.700 313.800
20 22 63 1 110.700 313.800
20 22 64 1 110.700 313.800
20 22 65 1 110.700 313.800
14 23 66 1 110.700 313.800
23 24 67 1 110.700 313.800
23 24 68 1 110.700 313.800
24 25 69 1 110.700 313.800
24 25 70 1 110.700 313.800
26 27 71 1 110.700 313.800
26 27 72 1 110.700 313.800
26 27 73 1 110.700 313.800
5 28 74 1 110.700 313.800
2 29 75 1 110.700 313.800
29 30 76 1 110.700 313.800
29 30 77 1 110.700 313.800
29 30 78 1 110.700 313.800
50 12 51 1 107.800 276.144
13 12 50 1 110.700 313.800
8 26 25 1 112.700 488.273
37 4 38 1 107.800 276.144
5 28 29 1 112.700 488.273
28 29 30 1 112.700 488.273
71 27 72 1 107.800 276.144
26 25 70 1 110.700 313.800
29 2 34 1 110.700 313.800
58 17 59 1 107.800 276.144
20 23 66 1 110.700 313.800
10 8 26 1 112.700 488.273
2 29 28 1 112.700 488.273
20 23 24 1 112.700 488.273
28 5 39 1 110.700 313.800
7 6 41 1 110.700 313.800
11 10 47 1 114.300 292.880
28 29 75 1 110.700 313.800
44 9 46 1 107.800 276.144
30 29 75 1 110.700 313.800
35 3 36 1 107.800 276.144
25 24 68 1 110.700 313.800
13 26 27 1 112.700 488.273
14 23 20 1 112.700 488.273
8 7 42 1 110.700 313.800
76 30 78 1 107.800 276.144
10 28 29 1 112.700 488.273
31 1 32 1 107.800 276.144
15 14 16 1 112.700 488.273
16 14 23 1 112.700 488.273
14 13 26 1 112.700 488.273
32 1 33 1 107.800 276.144
5 4 37 1 110.700 313.800
31 1 33 1 107.800 276.144
60 21 61 1 107.800 276.144
18 20 23 1 111.100 527.184
24 23 66 1 110.700 313.800
64 22 65 1 107.800 276.144
45 9 46 1 107.800 276.144
6 5 28 1 112.700 488.273
60 21 62 1 107.800 276.144
9 8 10 1 112.700 488.273
3 2 29 1 112.700 488.273
3 2 34 1 110.700 313.800
7 6 40 1 110.700 313.800
61 21 62 1 107.800 276.144
54 15 55 1 107.800 276.144
13 26 25 1 112.700 488.273
8 26 13 1 112.700 488.273
53 15 54 1 107.800 276.144
10 28 74 1 110.700 313.800
12 11 49 1 110.700 313.800
25 26 27 1 112.700 488.273
69 25 70 1 107.800 276.144
14 13 52 1 110.700 313.800
26 25 69 1 110.700 313.800
67 24 68 1 107.800 276.144
11 10 28 1 114.300 292.880
53 15 55 1 107.800 276.144
4 3 36 1 110.700 313.800
21 20 23 1 112.700 488.273
19 18 20 1 120.400 669.440
17 16 56 1 110.700 313.800
63 22 65 1 107.800 276.144
9 8 26 1 112.700 488.273
17 16 57 1 110.700 313.800
42 7 43 1 107.800 276.144
40 6 41 1 107.800 276.144
18 17 59 1 109.500 292.880
72 27 73 1 107.800 276.144
21 20 22 1 112.700 488.273
48 11 49 1 107.800 276.144
12 13 26 1 112.700 488.273
5 28 10 1 112.700 488.273
15 14 23 1 112.700 488.273
8 10 28 1 114.300 292.880
28 10 47 1 114.300 292.880
44 9 45 1 107.800 276.144
13 12 51 1 110.700 313.800
63 22 64 1 107.800 276.144
4 3 35 1 110.700 313.800
5 4 38 1 110.700 313.800
26 13 52 1 110.700 313.800
6 5 39 1 110.700 313.800
12 11 48 1 110.700 313.800
8 7 43 1 110.700 313.800
22 20 23 1 112.700 488.273
24 25 26 1 112.700 488.273
18 17 58 1 109.500 292.880
25 24 67 1 110.700 313.800
29 28 74 1 110.700 313.800
71 27 73 1 107.800 276.144
56 16 57 1 107.800 276.144
76 30 77 1 107.800 276.144
77 30 78 1 107.800 276.144
[dihedrals]
; IMPROPER DIHEDRAL ANGLES
; ai aj ak al funct c0 c1 c2 c3 c4 c5
20 18 17 19 4 180.000 43.932 2
[dihedrals]
; PROPER DIHEDRAL ANGLES
; ai aj ak al funct c0 c1 c2 c3 c4 c5
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [November 16, 2023, 5:41pm UTC](https://gromacs.bioexcel.eu/t/correcting-non-integral-charge-on-ligand/7652/5 "2023-11-16T17:41:24Z")
Without knowing what the structure is, I can’t really say. It is very bizarre to have so many different individual charges for something that appears to be composed of only C and H atoms. And only one dihedral? What is this molecule?
I can’t recommend a solution without far more information.
---
### Author:  [@KavyashreeM](https://gromacs.bioexcel.eu/u/KavyashreeM)
#### Post date: [November 17, 2023, 6:20am UTC](https://gromacs.bioexcel.eu/t/correcting-non-integral-charge-on-ligand/7652/6 "2023-11-17T06:20:50Z")
I could not attach the entire itp file due to the word limitation.
This is the molecule.
ATOM 1 C1 ZIN AC000 17.437 3.938 10.881 -0.43 +0.01
ATOM 2 C2 ZIN AC000 16.216 3.375 11.714 -0.54 -0.01
ATOM 3 C4 ZIN AC000 15.019 4.328 11.506 -0.35 +0.00
ATOM 4 C5 ZIN AC000 13.869 3.724 12.240 -0.39 +0.01
ATOM 5 C6 ZIN AC000 14.136 3.615 13.695 -0.22 +0.02
ATOM 6 C10 ZIN AC000 14.282 5.032 14.330 -0.23 +0.01
ATOM 7 C11 ZIN AC000 14.502 4.885 15.836 -0.18 +0.01
ATOM 8 C12 ZIN AC000 15.653 3.980 16.251 -0.26 -0.01
ATOM 9 C13 ZIN AC000 16.931 4.828 16.004 -0.48 +0.01
ATOM 10 C14 ZIN AC000 15.656 2.775 15.427 -0.21 -0.03
ATOM 11 C15 ZIN AC000 16.055 1.613 15.943 -0.20 -0.01
ATOM 12 C16 ZIN AC000 16.287 1.349 17.330 -0.16 +0.02
ATOM 13 C17 ZIN AC000 16.627 2.566 18.093 -0.30 +0.00
ATOM 14 C19 ZIN AC000 16.898 2.405 19.509 -0.31 -0.02
ATOM 15 C20 ZIN AC000 15.729 1.559 20.204 -0.23 +0.01
ATOM 16 C21 ZIN AC000 18.185 1.527 19.652 -0.50 +0.01
ATOM 17 C22 ZIN AC000 18.541 1.315 21.151 -0.50 +0.05
ATOM 18 C23 ZIN AC000 18.518 2.599 21.912 -0.42 +0.07
ATOM 19 O24 ZIN AC000 19.387 2.691 22.848 -0.22 -0.16
ATOM 20 C25 ZIN AC000 17.567 3.598 21.715 -0.42 +0.01
ATOM 21 C26 ZIN AC000 16.332 3.479 22.728 -0.33 +0.01
ATOM 22 C27 ZIN AC000 18.210 4.999 22.097 -0.44 +0.01
ATOM 23 C28 ZIN AC000 17.051 3.759 20.267 -0.38 +0.00
ATOM 24 C30 ZIN AC000 15.826 4.541 20.070 -0.27 +0.00
ATOM 25 C31 ZIN AC000 15.772 4.915 18.554 -0.18 +0.01
ATOM 26 C32 ZIN AC000 15.583 3.611 17.788 -0.21 -0.01
ATOM 27 C33 ZIN AC000 14.128 3.118 18.034 -0.07 +0.01
ATOM 28 C34 ZIN AC000 15.387 2.857 13.914 -0.26 +0.02
ATOM 29 C36 ZIN AC000 16.547 3.385 13.156 -0.47 -0.00
ATOM 30 C38 ZIN AC000 17.836 2.455 13.351 -0.41 +0.01
ATOM 31 C7 ZIN AC000 12.941 2.941 14.398 -0.11 +0.07
ATOM 32 O8 ZIN AC000 11.995 3.614 14.769 -0.00 -0.24
ATOM 33 O9 ZIN AC000 12.942 1.736 14.581 +0.04 -0.26
END