Atom HG in residue SER 25 was not found in rtp entry SER with 11 atoms while sorting atoms

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1

Hi I have tried using -ter but the result is like this:

Program: gmx pdb2gmx, version 2023.2-Homebrew
charmm36-jul2022.ff and -ter

Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 870)

Fatal error:

Atom HG in residue SER 25 was not found in rtp entry SER with 11 atoms

while sorting atoms.

For a hydrogen, this can be a different protonation state, or it

might have had a different number in the PDB file and was rebuilt

(it might for instance have been H3, and we only expected H1 & H2).

Note that hydrogens might have been added to the entry for the N-terminus.

Remove this hydrogen or choose a different protonation state to solve it.

Option -ignh will ignore all hydrogens in the input.

For more information and tips for troubleshooting, please check the GROMACS.

website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

I would like to know how to fix it.
Thanks You.

Best,
P

2

Did you modify SER 25 residue in PDB file?
I would check for any discrepancy for atom naming in SER 25, both between your input PDB file and the aminoacids.rtp file for SER.

3

I didn’t modify SER 25. How should I fix it?

4

@Panuwid did you follow the link provided in the error message or try -ignh as suggested? The solution is quite simple and has been asked and answered hundreds of times. Google is also your friend. You’ll find the answer immediately.

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