# Ligand parameterization for gromos96 force field **URL:** \ **Category:** User discussions\ **Tags:** forcefield\ **Created:** [September 13, 2024, 1:01am UTC](https://gromacs.bioexcel.eu/t/ligand-parameterization-for-gromos96-force-field/10148 "2024-09-13T01:01:34Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![nhina](https://avatars.discourse-cdn.com/v4/letter/n/46a35a/32.png) [@nhina](https://gromacs.bioexcel.eu/u/nhina)\ **Post date:** [September 13, 2024, 1:01am UTC](https://gromacs.bioexcel.eu/t/ligand-parameterization-for-gromos96-force-field/10148/1 "2024-09-13T01:01:34Z")
GROMACS version: 2019 GROMACS modification: Yes/No Here post your question Hi guys, I have a question related to ligand parameterization. I am working on protein-ligand complex simulation using gromacs version 2019.6. My protein is KLVFF which is a small sequence of amyloid. I used GROMOS96 54A7 to parameterize for protein. I am trying to parameterize for ligand following web tools ATB. However, when i run command “gmx grompp -f em.mdp -maxwarn 2 -c rec\_1.pdb -p top.top -o ion.tpr” to add ion, then it appears an error “Atomtype CAro not found”. I don’t know why gromos54a7 can not read MOL\_GMX.itp file created by ATB. Can you have any others option to parameterize ligand use other gromos96 force field? I hope some one can suggest me other option or how to fix this error. My top.top ; Created by: ; :-) GROMACS - gmx pdb2gmx, VERSION 2019.6 (-: ; ; Executable: /opt/gromacs/2019/bin/gmx ; Data prefix: /opt/gromacs/2019 ; Command line: ; gmx pdb2gmx -f KLVFF.pdb -ignh -p top.top -o rec.pdb -ter ; Force field was read from the standard GROMACS share directory. ; ; Include forcefield parameters #include “gromos54a7.ff/forcefield.itp” #include “MOL\_GMX.itp” ; Include chain topologies #include “top\_Protein\_chain\_A.itp” #include “top\_Protein\_chain\_A2.itp” ; Include water topology #include “gromos54a7.ff/spc.itp” #ifdef POSRES\_WATER ; Position restraint for each water oxygen [position\_restraints] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include “gromos54a7.ff/ions.itp” [system] ; Name Grunge ROck MAChoS in water [molecules] ; Compound #mols Protein\_chain\_A 1 Protein\_chain\_A2 1 NGOC 1 SOL 6227 Error: Thank you so much. Nhina. ---
**Author:** ![MBukharov](https://avatars.discourse-cdn.com/v4/letter/m/b487fb/32.png) [@MBukharov](https://gromacs.bioexcel.eu/u/MBukharov)\ **Post date:** [September 13, 2024, 9:51am UTC](https://gromacs.bioexcel.eu/t/ligand-parameterization-for-gromos96-force-field/10148/2 "2024-09-13T09:51:34Z")
Probably you need to write line #include “MOL\_GMX.itp” after protein topologies. Because NGOC appears after protein in [molecules] section and likely in .gro file. ---
**Author:** ![nhina](https://avatars.discourse-cdn.com/v4/letter/n/46a35a/32.png) [@nhina](https://gromacs.bioexcel.eu/u/nhina)\ **Post date:** [September 13, 2024, 11:52am UTC](https://gromacs.bioexcel.eu/t/ligand-parameterization-for-gromos96-force-field/10148/3 "2024-09-13T11:52:49Z")
Actually, i think it is not a key of this problem, because at the first time i write Include chain topologies #include “top\_Protein\_chain\_A.itp” #include “top\_Protein\_chain\_A2.itp” #include “MOL\_GMX.itp” but it still has the same error, so i think this error relating to force field. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 13, 2024, 1:46pm UTC](https://gromacs.bioexcel.eu/t/ligand-parameterization-for-gromos96-force-field/10148/4 "2024-09-13T13:46:38Z")
MOL\_GMX.itp seems to use atomtypes that are not specified in the force field. Do you get any other (itp) files from ATB? Do they contain an `[atomtypes]` section? ---
**Author:** ![nhina](https://avatars.discourse-cdn.com/v4/letter/n/46a35a/32.png) [@nhina](https://gromacs.bioexcel.eu/u/nhina)\ **Post date:** [September 13, 2024, 2:09pm UTC](https://gromacs.bioexcel.eu/t/ligand-parameterization-for-gromos96-force-field/10148/5 "2024-09-13T14:09:31Z")
ATB replied me with two itp files. One of them contains all atom and another contains united atom. However, in both of them don’t contain [atomtypes] section. They only contain sections as [atoms], [bonds], [pairs], [angles], [dihedrals], [dihedrals], [exclusions]. Does the lack of atomtypes affect reading the itp file? ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 13, 2024, 2:12pm UTC](https://gromacs.bioexcel.eu/t/ligand-parameterization-for-gromos96-force-field/10148/6 "2024-09-13T14:12:09Z")
The atomtype `CAro` is not defined in the standard Gromos force field (at least not the one that is shipped with GROMACS). So you will need to find the correct atom type data for that (and possibly other) atom type. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 13, 2024, 2:15pm UTC](https://gromacs.bioexcel.eu/t/ligand-parameterization-for-gromos96-force-field/10148/7 "2024-09-13T14:15:07Z")
From [https://mailman-1.sys.kth.se/pipermail/gromacs.org\_gmx-users/2020-March/128643.html:](https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2020-March/128643.html:) “ATB uses GROMOS 54a7 ATB, and you have to download and use that forcefield for any molecules you generate using that server. You cannot just mix it with GROMOS 53a6 like you have tried to, since 54a7\_atb has additional atom types.” It seems like you can download the 54a7\_atb force field from [https://atb.uq.edu.au/index.py?tab=forcefield\_files](https://atb.uq.edu.au/index.py?tab=forcefield_files). Edit: It is probably [https://atb.uq.edu.au/forcefield\_files/atb\_gromacs/5/gromos54a7\_atb.ff.tar.gz](https://atb.uq.edu.au/forcefield_files/atb_gromacs/5/gromos54a7_atb.ff.tar.gz) that you should download. ---
**Author:** ![nhina](https://avatars.discourse-cdn.com/v4/letter/n/46a35a/32.png) [@nhina](https://gromacs.bioexcel.eu/u/nhina)\ **Post date:** [September 13, 2024, 2:32pm UTC](https://gromacs.bioexcel.eu/t/ligand-parameterization-for-gromos96-force-field/10148/8 "2024-09-13T14:32:44Z")
Oh thank you very much. I will download the new force field and come back soon to give feedback. ---
**Author:** ![nhina](https://avatars.discourse-cdn.com/v4/letter/n/46a35a/32.png) [@nhina](https://gromacs.bioexcel.eu/u/nhina)\ **Post date:** [September 14, 2024, 3:58am UTC](https://gromacs.bioexcel.eu/t/ligand-parameterization-for-gromos96-force-field/10148/9 "2024-09-14T03:58:03Z")
I have successfully installed gromos 54a7\_atb forcefield and it runs smoothly. Thank you so much