Merged.hdb file needs improvement by this error appearance?

Hey guys,
I am using CHARMM36 for my catalase peotein.
I have gt this error

Does it mean that "merged.hdb " file must be edited?
how this can be solved?

Hi Sara, if you did not use it already, -ignh might help in forcing GROMACS to add back hyrdrogen atoms that are not found in your input pdb.

I did this but both missing atom warning and hydrogen errors remained. moreover, the simulation stopped in NPT step.

Hydrogen atoms are missing in the HEME group in your pdb file. You can add the hydrogen to the pdb (with the help of visualization program) or build an entry in merge.hdb for HEME group (for syntax see
Now gmx pdb2gmx does not know where to add the missing hydrogens, thus the option.
Best regards


I faced the same problem with a system containing a new residue and did that (-ignh and adding the H with another software). However, during the equilibration, the new residue falls apart, so I guess I have to necessarily update the merged.hdb, with the new hydrogens, right?


This is a general problem with any molecule - if the nomenclature of the atoms provided does not match the residue definition, either (1) you have to change the atom names in the input coordinate file or (2) use -ignh in conjunction with a suitable .hdb entry.

Dear Justin,
I changed the atom names based on merged.rtp file. however, the following message appeared.

Moreover, using -ignh causes the appearance of the missing atom error.

This is the same problem as before. You’re specifying an H atom in the input coordinates that is named incorrectly.

I changed the names of heme hydrogens as well as their order bas[Screenshot 2020-11-10 001644|356x499]

. Then, I imbedded them into the original PDB (1dgf). however, an error appeared:
there was a hydrogen name HMA1 and gromacs couldn’t recognized it. the error said that there is no residue under the name of MA!!!

Please post the actual error message.

Thank you for your response.
Following the use of -ignh , I got the error of missing atoms in HEME molecules.

Thank you for your response.
You mean trying embedding the Heme in my pdb into the merged.hdb?

The error means you’ve broken the PDB format by changing the required spacing of the columns. Editing the .hdb file would be very complicated for a molecule like heme. Renaming the atoms in the PDB is probably the easiest approach but you have to preserve the fixed-format nature of the PDB file.

you are right dear Justin.
But the problem is that I have tried different space patterns and I got similar errors. :( for exmple, I followed the spaces in the pdb but I got similar errors. Is it possible there it has something to do with four-character hydrogen names?
I tried three-character hydrogen names based on what is defined in the merged.hdb file. but again it showed an error. since it seems gromacs can only read the first hydrogen atoms : HA, HB, HC, and HD.

There is no problem with 4-character atom names. But the columns all have to be aligned properly. See, e.g.

Your spacing is simply incorrect for the HEM entries, causing a misinterpretation of the lines.

Dear Justin,
I appreciate your kind assistance. Following a precise modification of the PDB, it worked.
Thank You