# Problem in creating Topology by command pdb2gmx

**URL:** <https://gromacs.bioexcel.eu/t/problem-in-creating-topology-by-command-pdb2gmx/8509>\
**Category:** User discussions\
**Tags:** forcefield\
**Created:** [March 5, 2024, 10:45am UTC](https://gromacs.bioexcel.eu/t/problem-in-creating-topology-by-command-pdb2gmx/8509 "2024-03-05T10:45:11Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Papia33](https://avatars.discourse-cdn.com/v4/letter/p/58956e/32.png) [@Papia33](https://gromacs.bioexcel.eu/u/Papia33)\
**Post date:** [March 5, 2024, 10:45am UTC](https://gromacs.bioexcel.eu/t/problem-in-creating-topology-by-command-pdb2gmx/8509/1 "2024-03-05T10:45:11Z")

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GROMACS version:2018  
GROMACS modification: Yes/No  
Here post your question:  
I am getting following error with the command  
gmx pdb2gmx -f 2WGR\_clean.pdb -o 2WGR\_processed.gro -water spce  
HFatal error:  
Residue 163 named LYS of a molecule in the input file was mapped  
to an entry in the topology database, but the atom CG used in  
that entry is not found in the input file. Perhaps your atom  
and/or residue naming needs to be fixed.  
How to solve it?

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**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\
**Post date:** [March 5, 2024, 12:43pm UTC](https://gromacs.bioexcel.eu/t/problem-in-creating-topology-by-command-pdb2gmx/8509/2 "2024-03-05T12:43:38Z")

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The error is stating that there are atoms missing from one of the lysine residues of your protein. Examining the 2WGR pdb file, it seems the last lysine residue listed is missing several atoms. After a quick search, this [thread](https://www.researchgate.net/post/Fixing-missing-atoms-and-residues-in-PDB-file-before-using-pdb2gmx) suggests some software for manually fixing your proteins. There’s also a server which automates the process of fixing pdb files ([https://www.protein-science.com/](https://www.protein-science.com/)), the paper for which you can find here ([https://pubs.acs.org/doi/10.1021/acs.jcim.2c00571](https://pubs.acs.org/doi/10.1021/acs.jcim.2c00571))

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**Author:** ![Papia33](https://avatars.discourse-cdn.com/v4/letter/p/58956e/32.png) [@Papia33](https://gromacs.bioexcel.eu/u/Papia33)\
**Post date:** [March 6, 2024, 8:11am UTC](https://gromacs.bioexcel.eu/t/problem-in-creating-topology-by-command-pdb2gmx/8509/3 "2024-03-06T08:11:57Z")

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Thanks Karis. Your suggestion has solved the current problem. I have another issue. It will be nice if you can help me. I am facing problem in creatinh ligand topology. As per tutorial for GROMOS 96 force field we need PRODRG 2.5. This server is not working at all. ATB did not work for big size ligand. Please sugget how to create ligan topolgy for GROMOS 96?

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**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\
**Post date:** [March 6, 2024, 5:17pm UTC](https://gromacs.bioexcel.eu/t/problem-in-creating-topology-by-command-pdb2gmx/8509/4 "2024-03-06T17:17:47Z")

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You may need to generate topologies for individual fragments and using the parameters for those fragments to define the entire molecule, as suggested in the [FAQ](https://atb.uq.edu.au/index.py?tab=faq). The size limit on the ATB server is due to the limit in computational resources and there isn’t really a technical way to get around that.