How to fix additional hydrogen in gromacs??

12 February 2022 1 8K Report

How can I use ignh to ignore water molecules in a gromacs molecular dynamic simulation?

I would suggest you to attempt this. The error message may be suggesting that an entry in the hdb file is missing. More likely, the nomenclature of your hydrogen atoms simply does not match what is expected by the rtp entry. In this case, use -ignh to allow pdb2gmx to add the correct hydrogens for you, or re-name the problematic atoms.

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