# Protein-ligand complex tutorial errors

**URL:** <https://gromacs.bioexcel.eu/t/protein-ligand-complex-tutorial-errors/6056>\
**Category:** User discussions\
**Created:** [March 27, 2023, 9:46pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-tutorial-errors/6056 "2023-03-27T21:46:59Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![EOrfanakis](https://avatars.discourse-cdn.com/v4/letter/e/7cd45c/32.png) [@EOrfanakis](https://gromacs.bioexcel.eu/u/EOrfanakis)\
**Post date:** [March 27, 2023, 9:46pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-tutorial-errors/6056/1 "2023-03-27T21:46:59Z")

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GROMACS version:2023  
GROMACS modification: Yes/No  
Hello,  
I am a new user and tried to run a simple md simulation according to the protein ligand complex tutorial of gromacs. I edited the 3HTB pdb file, as the tutorial mentions.  
Specifically, i run:

1. grep JZ4 3HTB\_clean.pdb
2. grep -v HETATM 3HTB\_clean \> 3htb\_processed.pdb
3. gmx pdb2gmx -f 3htb\_processed.pdb -o 3htb\_processed.gro  
Then i choose CHARMM all-atom force field (which i downloaded and extracted to /gromacs/share/gromacs/top/) according to the tutorial, but i keep getting Fatal Errors such as:  
Fatal error:  
atom C1 not found in buiding block 1MET while combining tdb and rtp  
Fatal error:  
Atom type H1 (residue MET) not found in atomtype database  
Fatal error:  
Residue ‘HID’ not found in residue topology database  
I keep editting atomtypes.atp and aminoacids.rtp at the specific force field, but i wonder what am i doing wrong.  
Thank you very much for your time

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**Author:** ![jjmllen](https://avatars.discourse-cdn.com/v4/letter/j/e56c9b/32.png) [@jjmllen](https://gromacs.bioexcel.eu/u/jjmllen)\
**Post date:** [March 28, 2023, 2:14am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-tutorial-errors/6056/2 "2023-03-28T02:14:06Z")

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you need to prepare your protein first either use MOE or Swiss pdb viewer

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**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:** [March 28, 2023, 3:29am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-tutorial-errors/6056/3 "2023-03-28T03:29:42Z")

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> [@EOrfanakis](#):
>
> Fatal error:  
> atom C1 not found in buiding block 1MET while combining tdb and rtp  
> Fatal error:  
> Atom type H1 (residue MET) not found in atomtype database

The tutorial uses a slightly older version of the CHARMM36 port that did not have a certain terminal patch that screws up methionine. You need to interactively select the NH3+ terminus type with `-ter` added to the `pdb2gmx` command.

> [@EOrfanakis](#):
>
> I keep editting atomtypes.atp and aminoacids.rtp at the specific force field, but i wonder what am i doing wrong.

You should not have to make any changes to force field files.

> [@jjmllen](#):
>
> you need to prepare your protein first either use MOE or Swiss pdb viewer

This is unnecessary. The tutorial should work cleanly without any real extra effort with outside programs. I will probably update it soon for those users who are using the July 2022 CHARMM36 port. The tutorial uses one from March 2019 (which is still available online, so the tutorial **can** be completed as written).

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**Author:** ![EOrfanakis](https://avatars.discourse-cdn.com/v4/letter/e/7cd45c/32.png) [@EOrfanakis](https://gromacs.bioexcel.eu/u/EOrfanakis)\
**Post date:** [April 3, 2023, 10:11am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-tutorial-errors/6056/4 "2023-04-03T10:11:48Z")

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> [@jalemkul](#):
>
> The tutorial uses a slightly older version of the CHARMM36 port that did not have a certain terminal patch that screws up methionine. You need to interactively select the NH3+ terminus type with `-ter` added to the `pdb2gmx` command.

Thank you very much, that fixed my problem!