1. How to generate ligand(hetero group) .gro file .itp file and .prm file for Amber and OPLS force

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  1. How to generate ligand(hetero group) .gro file .itp file and .prm file for Amber and OPLS force field? I tried from acpype and ligpargen server but donot work? Is there any tutorial?

From ligpargen atomtype start from opls-800

;
; GENERATED BY LigParGen Server
; Jorgensen Lab @ Yale University
;
[ atomtypes ]
opls_857 H857 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_868 C868 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_851 O851 15.9990 0.000 A 2.96000E-01 8.78640E-01
opls_831 H831 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_806 H806 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_861 C861 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_838 H838 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_866 C866 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_840 C840 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_836 H836 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_813 H813 1.0080 0.000 A 2.50000E-01 1.25520E-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_834 C834 12.0110 0.000 A 3.55000E-01 3.17984E-01
opls_873 H873 1.0080 0.000 A 2.42000E-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_871 H871 1.0080 0.000 A 2.42000E-01 1.25520E-01
opls_809 C809 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_830 H830 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_818 O818 15.9990 0.000 A 3.12000E-01 7.11280E-01
opls_803 C803 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_821 O821 15.9990 0.000 A 3.12000E-01 7.11280E-01
opls_856 H856 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_805 H805 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_814 O814 15.9990 0.000 A 2.90000E-01 5.85760E-01
opls_849 C849 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_847 H847 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_820 H820 1.0080 0.000 A 2.50000E-01 1.25520E-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_854 H854 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_869 H869 1.0080 0.000 A 2.42000E-01 1.25520E-01
opls_810 H810 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_845 H845 1.0080 0.000 A 2.42000E-01 1.25520E-01
opls_816 H816 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_858 H858 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_801 O801 15.9990 0.000 A 3.12000E-01 7.11280E-01
opls_829 C829 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_815 C815 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_850 C850 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_823 H823 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_800 H800 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_819 C819 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_852 O852 15.9990 0.000 A 2.90000E-01 5.85760E-01
opls_839 C839 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_843 O843 15.9990 0.000 A 2.90000E-01 5.85760E-01
opls_841 H841 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_833 C833 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_827 C827 12.0110 0.000 A 3.55000E-01 3.17984E-01
opls_870 O870 15.9990 0.000 A 2.90000E-01 5.85760E-01
opls_864 H864 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_832 C832 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_822 H822 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_846 C846 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_844 O844 15.9990 0.000 A 2.96000E-01 8.78640E-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_807 O807 15.9990 0.000 A 2.90000E-01 5.85760E-01
opls_804 H804 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_872 C872 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_865 H865 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_867 C867 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_826 H826 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_853 C853 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_811 O811 15.9990 0.000 A 3.12000E-01 7.11280E-01
opls_817 H817 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_859 H859 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_842 C842 12.0110 0.000 A 3.55000E-01 2.92880E-01
[ moleculetype ]
; Name nrexcl
LPA 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_800 1 LPA H00 1 0.4116 1.0080
2 opls_801 1 LPA O01 1 -0.5774 15.9990
3 opls_802 1 LPA C02 1 0.0242 12.0110
4 opls_803 1 LPA C03 1 0.0451 12.0110
5 opls_804 1 LPA H04 1 0.0904 1.0080
6 opls_805 1 LPA H05 1 0.0904 1.0080
7 opls_806 1 LPA H06 1 0.0922 1.0080
8 opls_807 1 LPA O07 1 -0.3777 15.9990
9 opls_808 1 LPA C08 1 0.0052 12.0110
10 opls_809 1 LPA C09 1 0.2135 12.0110
11 opls_810 1 LPA H0A 1 0.1694 1.0080
12 opls_811 1 LPA O0B 1 -0.5584 15.9990
13 opls_812 1 LPA C0C 1 0.0365 12.0110
14 opls_813 1 LPA H0D 1 0.1314 1.0080
15 opls_814 1 LPA O0E 1 -0.3706 15.9990
16 opls_815 1 LPA C0F 1 -0.0298 12.0110
17 opls_816 1 LPA H0G 1 0.4059 1.0080
18 opls_817 1 LPA H0H 1 0.1413 1.0080
19 opls_818 1 LPA O0I 1 -0.5514 15.9990
20 opls_819 1 LPA C0J 1 0.0844 12.0110
21 opls_820 1 LPA H0K 1 0.1310 1.0080
22 opls_821 1 LPA O0M 1 -0.5652 15.9990
23 opls_822 1 LPA H0N 1 0.4172 1.0080
24 opls_823 1 LPA H0O 1 0.0902 1.0080
25 opls_824 1 LPA C0P 1 0.0319 12.0110
26 opls_825 1 LPA C0Q 1 -0.1982 12.0110
27 opls_826 1 LPA H0R 1 0.4184 1.0080
28 opls_827 1 LPA C0S 1 -0.1314 12.0110
29 opls_828 1 LPA C0T 1 -0.2398 12.0110
30 opls_829 1 LPA C0U 1 -0.0840 12.0110
31 opls_830 1 LPA H0V 1 0.1376 1.0080
32 opls_831 1 LPA H0W 1 0.1376 1.0080
33 opls_832 1 LPA C0X 2 -0.1678 12.0110
34 opls_833 1 LPA C0Y 2 0.5025 12.0110
35 opls_834 1 LPA C0Z 2 -0.1387 12.0110
36 opls_835 1 LPA H10 2 0.0966 1.0080
37 opls_836 1 LPA H11 2 0.0966 1.0080
38 opls_837 1 LPA H12 2 0.0966 1.0080
39 opls_838 1 LPA H13 2 0.0967 1.0080
40 opls_839 1 LPA C14 2 -0.1672 12.0110
41 opls_840 1 LPA C15 2 -0.0285 12.0110
42 opls_841 1 LPA H16 2 0.1449 1.0080
43 opls_842 1 LPA C17 2 0.4786 12.0110
44 opls_843 1 LPA O18 2 -0.3469 15.9990
45 opls_844 1 LPA O19 2 -0.4308 15.9990
46 opls_845 1 LPA H1A 2 0.1534 1.0080
47 opls_846 1 LPA C1B 2 -0.1474 12.0110
48 opls_847 1 LPA H1C 2 0.0930 1.0080
49 opls_848 1 LPA H1D 2 0.0930 1.0080
50 opls_849 1 LPA C1E 2 -0.2353 12.0110
51 opls_850 1 LPA C1F 2 -0.2227 12.0110
52 opls_851 1 LPA O1G 2 -0.4288 15.9990
53 opls_852 1 LPA O1H 2 -0.3807 15.9990
54 opls_853 1 LPA C1I 2 -0.0567 12.0110
55 opls_854 1 LPA H1J 2 0.1037 1.0080
56 opls_855 1 LPA H1K 2 0.1037 1.0080
57 opls_856 1 LPA H1M 2 0.0936 1.0080
58 opls_857 1 LPA H1N 2 0.0936 1.0080
59 opls_858 1 LPA H1O 2 0.0936 1.0080
60 opls_859 1 LPA H1P 2 0.1174 1.0080
61 opls_860 1 LPA H1Q 2 0.1174 1.0080
62 opls_861 1 LPA C1R 2 0.1959 12.0110
63 opls_862 1 LPA H1S 2 0.1005 1.0080
64 opls_863 1 LPA H1T 2 0.1005 1.0080
65 opls_864 1 LPA H1U 2 0.1005 1.0080
66 opls_865 1 LPA H1V 3 0.1199 1.0080
67 opls_866 1 LPA C1W 3 -0.1871 12.0110
68 opls_867 1 LPA C1X 3 -0.0804 12.0110
69 opls_868 1 LPA C1Y 3 -0.1907 12.0110
70 opls_869 1 LPA H1Z 3 0.2151 1.0080
71 opls_870 1 LPA O20 3 -0.1489 15.9990
72 opls_871 1 LPA H21 3 0.2039 1.0080
73 opls_872 1 LPA C22 3 -0.0964 12.0110
74 opls_873 1 LPA H23 3 0.2222 1.0080
[ bonds ]
2 1 1 0.0945 462750.400
3 2 1 0.1410 267776.000
4 3 1 0.1529 224262.400
5 3 1 0.1090 284512.000
6 3 1 0.1090 284512.000
7 4 1 0.1090 284512.000
8 4 1 0.1410 267776.000
9 4 1 0.1529 224262.400
10 8 1 0.1380 267776.000
11 9 1 0.1090 284512.000
12 9 1 0.1410 267776.000
13 9 1 0.1529 224262.400
14 10 1 0.1090 284512.000
15 10 1 0.1380 267776.000
16 10 1 0.1529 224262.400
17 12 1 0.0945 462750.400
18 13 1 0.1090 284512.000
19 13 1 0.1410 267776.000
20 15 1 0.1410 267776.000
21 16 1 0.1090 284512.000
22 16 1 0.1410 267776.000
23 19 1 0.0945 462750.400
24 20 1 0.1090 284512.000
25 20 1 0.1529 224262.400
26 20 1 0.1529 224262.400
27 22 1 0.0945 462750.400
28 25 1 0.1510 265265.600
29 25 1 0.1529 224262.400
30 25 1 0.1529 224262.400
31 26 1 0.1090 284512.000
32 26 1 0.1090 284512.000
33 26 1 0.1529 224262.400
34 28 1 0.1444 343088.000
35 28 1 0.1340 459403.200
36 29 1 0.1090 284512.000
37 29 1 0.1090 284512.000
38 29 1 0.1090 284512.000
39 30 1 0.1090 284512.000
40 30 1 0.1529 224262.400
41 30 1 0.1529 224262.400
42 33 1 0.1090 284512.000
43 33 1 0.1522 265265.600
44 34 1 0.1327 179075.200
45 34 1 0.1229 476976.000
46 35 1 0.1080 307105.600
47 35 1 0.1510 265265.600
48 40 1 0.1090 284512.000
49 40 1 0.1090 284512.000
50 41 1 0.1529 224262.400
51 41 1 0.1529 224262.400
52 43 1 0.1229 476976.000
53 43 1 0.1327 179075.200
54 44 1 0.1410 267776.000
55 47 1 0.1090 284512.000
56 47 1 0.1090 284512.000
57 50 1 0.1090 284512.000
58 50 1 0.1090 284512.000
59 50 1 0.1090 284512.000
60 51 1 0.1090 284512.000
61 51 1 0.1090 284512.000
62 51 1 0.1529 224262.400
63 54 1 0.1090 284512.000
64 54 1 0.1090 284512.000
65 54 1 0.1090 284512.000
66 62 1 0.1090 284512.000
67 62 1 0.1495 265265.600
68 67 1 0.1367 456892.800
69 67 1 0.1424 392459.200
70 68 1 0.1080 307105.600
71 68 1 0.1360 284512.000
72 69 1 0.1080 307105.600
73 69 1 0.1367 456892.800
74 73 1 0.1080 307105.600
16 13 1 0.1529 224262.400
41 33 1 0.1529 224262.400
47 40 1 0.1529 224262.400
62 53 1 0.1410 267776.000
73 71 1 0.1360 284512.000

[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 3 1 108.500 460.240
2 3 4 1 109.500 418.400

The logic is identical to the procedure given in Protein-Ligand Complex

Hi,

What you uploaded is a topol.top file for a molecule, but which is your question?

Please avoid to include the topol file in this way. use a link
Best regards

Alessandra

Thank You Sir, This tutorial focus on Cgenff server to create topology file of ligand for Charmm force field. But I want to use opls force field and amber force field. For these I use ligpargen and acpype server but I couldn’t create compatible topology file of ligand. I got atoms error(example : atomtype opls_800 not found). How can I solve it?

Ok maam

Then the server should provide modified force field files that define non-standard atom types, or you should contact their developers to alert them of the non-existent type (this has happened with LigParGen before, as discussed in this forum).

Thank you for your kind reply