Modifications All-Atom Problem

[fgrunewald]

@pckroon if you look in AllAtomProteins/1MJ5/vermouth you will find molecule.itp and out.pdb. In ../gmx/charmm36-jul2022.ff/modificatins_protonation.ff are the modification files. Interestingly for the HIS-HE modification all coordinates are deleted while there are strange doubling of coordinates for the others. When you run it there will also be a warning about stacking modifications.

Command

martinize2 -f ../1mj5_all_hydrogen.pdb -ff-dir ../gmx/ -ff charmm36-jul2022.ff -noscfix -from charmm36-jul2022.ff -x out.pdb -o topol.top -ignore SOL -maxwarn 2

[fgrunewald]

@pckroon