Fatal error: Residue 169 named LYS of a molecule in the input file was mapped to an entry in the top

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Hello everyone
I am beginner to gromacs, i want simulate protein ligand using OPLS-AA/L force field . But when i do pdb2gmx , it gives me the following error:

Fatal error:
Residue 169 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CD used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

please how to fix this

Regards,
Nandhini

2

You have a missing atom that needs to be built back in before pdb2gmx can process the coordinates and write the topology.

1 Like
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Thank you

4

how to build build missing atoms?

5

Modeller is one choice, but there are also simpler online webservers for that.