# Grompp with alternative ligands, adding to ff

**URL:** <https://gromacs.bioexcel.eu/t/grompp-with-alternative-ligands-adding-to-ff/4014>\
**Category:** User discussions\
**Tags:** forcefield, grompp\
**Created:** [April 13, 2022, 11:49am UTC](https://gromacs.bioexcel.eu/t/grompp-with-alternative-ligands-adding-to-ff/4014 "2022-04-13T11:49:14Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\
**Post date:** [April 13, 2022, 11:49am UTC](https://gromacs.bioexcel.eu/t/grompp-with-alternative-ligands-adding-to-ff/4014/1 "2022-04-13T11:49:14Z")

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GROMACS version:2022  
GROMACS modification: No  
Here post your question

I have a protein with a nonstandard substrate validol and guanosine di phosphate. I am using CHARMM36-2021 ff along with a cgenff .str that was modified according to the protein-ligand tuitorial by justin Lemkul and subjected to the charm2gmx script to produce .itp file and a prm. The script commented that I need to " Additional parameters needed by the molecule are written to va7p.prm, which needs to be included in the system .top"

I did not add the prm and ran into issues running grompp for assembling a ions.tpr to begin energy min.

ERROR 1 [file va7p.itp, line 248]:  
No default Proper Dih. types

ERROR 6 [file gdpv.itp, line 309]:  
No default U-B types

ERROR 41 [file va7p.itp, line 5]:  
moleculetype VA7P is redefined

I want clarification that my applying the .prm to the bondedd.ff of my charm36ff will resolve the " No default Proper Dih. types" error and in line 5 of my va7p is just the molecule name VA7P. is it the change in letter case thats causing a problem?

Could you please help me to solve this??

Thanks, in advance.

With regards,  
Derek

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<div class="post-metadata">

**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\
**Post date:** [April 13, 2022, 2:55pm UTC](https://gromacs.bioexcel.eu/t/grompp-with-alternative-ligands-adding-to-ff/4014/2 "2022-04-13T14:55:09Z")

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I went over things and the problem was my .prm files were not properly labeled in the topology file. same with my VA7P itp.