How to deal with hydrogen in pdb2gmx

User discussions
1

hi i have run pdb2gmx for protein topology and the error is coming for hydrogen. I don’t know if -ignh flag should be used or not

End terminus HIS-525: COO-
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 790)

Fatal error:
Atom HD1 in residue HIS 20 was not found in rtp entry HSE with 17 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 http://www.gromacs.org/Documentation/Errors
2

As mentioned in your error message add ignore hydrogens to your command, this may resolve the issue
gmx pdb2gmx -f input.pdb -o output.gro -water spce -ignh

When working with PDB files, especially those from NMR structures, it’s often more convenient to disregard hydrogen (H) atoms. This is because, if hydrogen atoms are included, they need to be named exactly as specified by the force fields in GROMACS. Since naming conventions for hydrogen atoms vary, this can sometimes cause complications. If you want to keep the original coordinates of hydrogen atoms but need to rename them, the sed command in Linux can be a useful tool for this purpose.

3

I have a modelled structure and don’t know whether hydrogen play important role in protein or not

4

If the protein is modeled, the positions of the H atoms are the least concerning consideration in whether or not the model is reasonable. Use -ignh and reconstruct them with the appropriate names.

5

i used a protein-ligand complex after getting it from autodockVina i.e after docking. The ligand bound with this protein is designed by me. I did docking and after that i got the complex with best score. Then i input in gromacs. My question is that whether i need to process it again by removing water and het atom? And i also got an error like this
“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.”
please help, iam new to this

6

ya you can use -ignh then your error will be solved