GROMACS version:2020
GROMACS modification: Yes/No
Thank you. I feel confused for how to designate the protonated stage of amino acid using the pdb2gmax. If the Asp is protonized, how to set the parameter to tell program its stage. I mean the default format is -[[no] asp], if I want to change the option, should I change it into the following format, -[yes]asp for using the option? And the his has three stages, how to specify its stage using the -[[no]his]. Also, for disulfide, -[[no]ss], How do you change its parameters specifically to tell the program which cysteines form disulfide bonds? Thank you very much.
gmx pdb2gmx [-f [<.gro/.g96/…>]] [-o [<.gro/.g96/…>]] [-p [<.top>]]
[-i [<.itp>]] [-n [<.ndx>]] [-q [<.gro/.g96/…>]]
[-chainsep ] [-merge ] [-ff ]
[-water ] [-[no]inter] [-[no]ss] [-[no]ter]
[-[no]lys] [-[no]arg] [-[no]asp] [-[no]glu] [-[no]gln]
[-[no]his] [-angle ] [-dist ] [-[no]una]
[-[no]ignh] [-[no]missing] [-[no]v] [-posrefc ]
[-vsite ] [-[no]heavyh] [-[no]deuterate]
[-[no]chargegrp] [-[no]cmap] [-[no]renum] [-[no]rtpres]