| ENERGY MINIMIZATION MOLECULAR DYNAMICS |
ENERGY MINIMISATION. A DISTANT DEPENDENT DIELECTRIC CONSTANT EQUAL TO 4R WAS APPLIED. THE NET
ELECTRIC CHARGES WERE DECREASED, WHILE THOSE OF THE N AND C TERMINAL CHARGED
GROUPS WERE NEGLECTED. IN THE PDB, NH3+ IS INCLUDED IN THE RESIDUE CYS, AND
COO- IS INCLUDED IN THE RESIDUE ALA. THE RESIDUE GLU HAS MISSING ATOMS HE2 IN ALL STRUCTURES
BECAUSE IN DISCOVER, THIS RESIDUE IS MODELLED AS A CHARGED GROUP(WE HAVE COO- AND NOT COOH). |
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