Martinize: Charged Histidine residue incorrectly defined

[biomolsim]

Cross-posting from the Martini forum

Hello everyone,

I came across an issue with "martinize.py" when I ran an MD simulation. Although "martinize.py" is able to detect the HIH residue as an input option, but while writing the ITP file, it is missing the positively charged (+1) D atom from the charged histidine residue.

As a result, there is an inconsistency between the output PDB and ITP files, since the PDB file indeed contains the additional atom too.

Please have a look at this Matini aminoacid topology file.

The following command was passed to the "martinize.py" module.

python3 martinize.py -f prot.pdb -dssp /usr/bin/dssp -ff elnedyn22p -ef 500 -eu 0.90 -p All -name cg_prot -n cg_prot.ndx -nmap fa_cg_prot.map -x cg_prot.pdb -o cg_prot.top

Thank you very much for reading my query.