# 1. How to generate ligand(hetero group) .gro file .itp file and .prm file for Amber and OPLS force **URL:** \ **Category:** User discussions\ **Tags:** forcefield\ **Created:** [April 12, 2021, 1:50am UTC](https://gromacs.bioexcel.eu/t/1-how-to-generate-ligand-hetero-group-gro-file-itp-file-and-prm-file-for-amber-and-opls-force/1940 "2021-04-12T01:50:14Z")\ **Posts on this page:** 11\ **Page:** 1
**Author:** ![Santosh456](https://avatars.discourse-cdn.com/v4/letter/s/a8b319/32.png) [@Santosh456](https://gromacs.bioexcel.eu/u/Santosh456)\ **Post date:** [April 12, 2021, 1:50am UTC](https://gromacs.bioexcel.eu/t/1-how-to-generate-ligand-hetero-group-gro-file-itp-file-and-prm-file-for-amber-and-opls-force/1940/1 "2021-04-12T01:50:15Z")
GROMACS version: GROMACS modification: Yes/No Here post your question 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? ---
**Author:** ![Santosh456](https://avatars.discourse-cdn.com/v4/letter/s/a8b319/32.png) [@Santosh456](https://gromacs.bioexcel.eu/u/Santosh456)\ **Post date:** [April 13, 2021, 3:25pm UTC](https://gromacs.bioexcel.eu/t/1-how-to-generate-ligand-hetero-group-gro-file-itp-file-and-prm-file-for-amber-and-opls-force/1940/3 "2021-04-13T15:25:00Z")
From ligpargen atomtype start from opls-800 ---
**Author:** ![Santosh456](https://avatars.discourse-cdn.com/v4/letter/s/a8b319/32.png) [@Santosh456](https://gromacs.bioexcel.eu/u/Santosh456)\ **Post date:** [April 14, 2021, 12:50pm UTC](https://gromacs.bioexcel.eu/t/1-how-to-generate-ligand-hetero-group-gro-file-itp-file-and-prm-file-for-amber-and-opls-force/1940/4 "2021-04-14T12:50:49Z")
; ; 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 ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [April 14, 2021, 1:43pm UTC](https://gromacs.bioexcel.eu/t/1-how-to-generate-ligand-hetero-group-gro-file-itp-file-and-prm-file-for-amber-and-opls-force/1940/6 "2021-04-14T13:43:41Z")
The logic is identical to the procedure given in [Protein-Ligand Complex](http://www.mdtutorials.com/gmx/complex/index.html) ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [April 14, 2021, 1:44pm UTC](https://gromacs.bioexcel.eu/t/1-how-to-generate-ligand-hetero-group-gro-file-itp-file-and-prm-file-for-amber-and-opls-force/1940/7 "2021-04-14T13:44:08Z")
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 ---
**Author:** ![Santosh456](https://avatars.discourse-cdn.com/v4/letter/s/a8b319/32.png) [@Santosh456](https://gromacs.bioexcel.eu/u/Santosh456)\ **Post date:** [April 14, 2021, 2:12pm UTC](https://gromacs.bioexcel.eu/t/1-how-to-generate-ligand-hetero-group-gro-file-itp-file-and-prm-file-for-amber-and-opls-force/1940/8 "2021-04-14T14:12:50Z")
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? ---
**Author:** ![Santosh456](https://avatars.discourse-cdn.com/v4/letter/s/a8b319/32.png) [@Santosh456](https://gromacs.bioexcel.eu/u/Santosh456)\ **Post date:** [April 14, 2021, 2:13pm UTC](https://gromacs.bioexcel.eu/t/1-how-to-generate-ligand-hetero-group-gro-file-itp-file-and-prm-file-for-amber-and-opls-force/1940/9 "2021-04-14T14:13:09Z")
Ok maam ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [April 14, 2021, 2:24pm UTC](https://gromacs.bioexcel.eu/t/1-how-to-generate-ligand-hetero-group-gro-file-itp-file-and-prm-file-for-amber-and-opls-force/1940/10 "2021-04-14T14:24:31Z")
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). ---
**Author:** ![Santosh456](https://avatars.discourse-cdn.com/v4/letter/s/a8b319/32.png) [@Santosh456](https://gromacs.bioexcel.eu/u/Santosh456)\ **Post date:** [April 14, 2021, 2:40pm UTC](https://gromacs.bioexcel.eu/t/1-how-to-generate-ligand-hetero-group-gro-file-itp-file-and-prm-file-for-amber-and-opls-force/1940/11 "2021-04-14T14:40:19Z")
Thank you for your kind reply ---
**Author:** ![alanwilter](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alanwilter/32/627_2.png) [@alanwilter](https://gromacs.bioexcel.eu/u/alanwilter)\ **Post date:** [December 12, 2021, 8:38am UTC](https://gromacs.bioexcel.eu/t/1-how-to-generate-ligand-hetero-group-gro-file-itp-file-and-prm-file-for-amber-and-opls-force/1940/12 "2021-12-12T08:38:52Z")
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](https://github.com/alanwilter/acpype). There are some tutorials in the wiki pages and I’m updating the old ones. ---
**Author:** ![khedrghada](https://avatars.discourse-cdn.com/v4/letter/k/ea666f/32.png) [@khedrghada](https://gromacs.bioexcel.eu/u/khedrghada)\ **Post date:** [September 6, 2024, 12:20am UTC](https://gromacs.bioexcel.eu/t/1-how-to-generate-ligand-hetero-group-gro-file-itp-file-and-prm-file-for-amber-and-opls-force/1940/13 "2024-09-06T00:20:49Z")
Did you find solution for this error?