Dear CHARMM users,
I have a question about the structure distorsion due to the addition of hydrogen atoms.
With the structure of a protein molecule which doesn't contain any hydrogen atom, I used CHARMM to add hydrogens. The problem that I have here is, the positions of some hydrogen atoms are not put in appropriate positions. For example, the +NH2=C-NH2 terminus of some ARG residue are not planar as expected. Minimization of either hydrogen atoms or side chains couldn't correct this distorsion. I also tried to use SYBYL to add hydrogens instead of CHARMM, and the same problem happens. Does anybody know how to solve this problem?
Any suggestion and help will be highly appreciated.