# Adding a new residue to topology

**URL:** <https://gromacs.bioexcel.eu/t/adding-a-new-residue-to-topology/1918>\
**Category:** User discussions\
**Tags:** pdb2gmx\
**Created:** [April 8, 2021, 7:06am UTC](https://gromacs.bioexcel.eu/t/adding-a-new-residue-to-topology/1918 "2021-04-08T07:06:54Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![yasser.almeida](https://avatars.discourse-cdn.com/v4/letter/y/76d3ee/32.png) [@yasser.almeida](https://gromacs.bioexcel.eu/u/yasser.almeida)\
**Post date:** [April 8, 2021, 7:06am UTC](https://gromacs.bioexcel.eu/t/adding-a-new-residue-to-topology/1918/1 "2021-04-08T07:06:54Z")

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GROMACS version: 2020.1  
GROMACS modification:

Hello,

I want to run a host-ligand simulation with CHARMM36 FF. The parameters of the ligand (PRG) were obtained before and stored as CHARMM .prm file. Then, I used TopoTools in VMD (with the `writegmxtop` function) to obtain the ligand’s parameters/topology as an .itp file. With this I want to build the topology for the complex. When I run pdb2gmx (`gmx pdb2gmx -f complex.pdb -o complex.gro -p complex_topol.top -i PRG.itp -water tip3p`) I get:

```
Fatal error:
Residue 'PRG' not found in residue topology database

```

Is there any way to override the inclusion of the new residue in the .rtp file and just `#include` it in the topology?

Thanks in advance.

Best regards

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<div class="post-metadata">

**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 8, 2021, 12:57pm UTC](https://gromacs.bioexcel.eu/t/adding-a-new-residue-to-topology/1918/2 "2021-04-08T12:57:46Z")

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See [Protein-Ligand Complex](http://www.mdtutorials.com/gmx/complex/index.html)