Use `-ignh` to fix error for missing hydrogen atoms...HOW?

User discussions
1

GROMACS version:GROMACS/2018.4
GROMACS modification: No
How do I incorporate -ignh to allow the system to add the correct hydrogens for me? any info will be helpful!

I got the following error message:

Missing hydrogen atoms; 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.

2

Hi,
One thing that the error message suggests to preprocess your original structure using the tool gmx pdb2gmx together with the option -ignh
Does it work?
\Alessandra

3

Thank you, I have not tried that yet but will today to see if it works. I was not sure where to include -ignh but now that you mention preprocess that guides me somewhat.

Thanks!

5

It did work!