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

Are you still having this issue with ACPYPE? You don’t say which ACPYPE version you’re using neither the command you’re issued.

If asking for help with ACPYPE, please, always rerun it with -d and send the detailed output.

Try to use the latest version seen here. There are some tutorials in the wiki pages and I’m updating the old ones.