Res 'HIS' is converted into 'X' after protonation

User discussions
1

GROMACS version:2022.2
GROMACS modification: Yes/No
@jalemkul
I am using CHARMM36-mar2019 for Protein-Protein MD simulation.
For the protonation of ‘HIS’ I am converting pdb into pqr using **pdb2pqr30** at pH=7.
Next I’m assigning charges manually using command pdb2gmx -f xyz.pdb -o xyz.gro -water tip3p -ignh -merge all -ff charmm36-mar2019 -his.
xyz.gro has HISD and HISE Residues which is obvious.

Problem:
Upon visualizing .gro or MD movie, it shows ‘X’ instead of ‘HIS’. Is it okay to go with the MD simulation? Does this impact the simulation?

2

I have never heard of a residue name being converted to X by any GROMACS tool, so this doesn’t make sense to me.

3

Thanks, Then I think its a problem of Chimera. It is not able to recognize HISD and HISE residues.

4

Hi,
you can add -inter flag for modifying the protonation state of His.