# Itp ligand file generation

**URL:** <https://ask.bioexcel.eu/t/itp-ligand-file-generation/2818>\
**Category:** pmx\
**Created:** [February 9, 2021, 10:34pm UTC](https://ask.bioexcel.eu/t/itp-ligand-file-generation/2818 "2021-02-09T22:34:08Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![gian93](https://avatars.discourse-cdn.com/v4/letter/g/cab0a1/32.png) [@gian93](https://ask.bioexcel.eu/u/gian93)\
**Post date:** [February 9, 2021, 10:34pm UTC](https://ask.bioexcel.eu/t/itp-ligand-file-generation/2818/1 "2021-02-09T22:34:08Z")

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Dear all,  
In the pmx tutorial, it is described a workflow for thermodynamic integration of ligand. For the generation of the double topologies a gromacs file \*.itp is required: is there a way to write it? I previously parametrized my system with tleap in order to use Amber force field. So my gromacs topology file has all the solute atoms in a single group since I used the Acpype parser to obtain input file for MD simulations. Do I have to select by hand all the ligand parameters or is there a simpler way?  
Thanks for the help

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**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\
**Post date:** [September 30, 2021, 1:26pm UTC](https://ask.bioexcel.eu/t/itp-ligand-file-generation/2818/2 "2021-09-30T13:26:45Z")

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I recommend using pdb2gmx to generate topologies for protein. The ligand topologies then can be created with acpype+antechamber combination.

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**Author:** ![gian93](https://avatars.discourse-cdn.com/v4/letter/g/cab0a1/32.png) [@gian93](https://ask.bioexcel.eu/u/gian93)\
**Post date:** [October 6, 2021, 8:20pm UTC](https://ask.bioexcel.eu/t/itp-ligand-file-generation/2818/3 "2021-10-06T20:20:05Z")

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I can generate the protein as well through the Amber _tleap_ module. Instead, with the combination acype+antechamber I can generate a \*top and \*gro files with just the ligand. How the \*itp with just ligand parameters is generated?

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<div class="post-metadata">

**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\
**Post date:** [October 14, 2021, 2:34pm UTC](https://ask.bioexcel.eu/t/itp-ligand-file-generation/2818/4 "2021-10-14T14:34:59Z")

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.itp file is similar to .top, it just contains entries relevant for the given molecule, e.g. moleculetype, atoms, bonds, angles, dihedrals, etc.

You can find more information in the Gromacs manual: [File formats — GROMACS 2021.3 documentation](https://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#molecule-itp-file)