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IO_file_MM-formats
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
IO INPUT FORMAT FILE
================================================================================
input.pdb
================================================================================
System Characteristics fmt(a72)
CRYST1 T_x T_y T_z fmt(t10, f6.3, t19, f6.3, t28, f6.3)
WORD 1 MMSymbol residue nr x y z Symbol
WORD 2 . . . . . . .
WORD 3 . . . . . . . fmt(t12,a5,t18,a3,t23,i7,t31,f8.3,t39,f8.3,t47,f8.3,t77,a2)
WORD . . . . . . . .
WORD . . . . . . . .
MASTER
END
================================================================================
potential.inpt
================================================================================
Force field ( 1 = Born Meyer , 2 = LJ )
CombinationRule ( 2 = AMBER , 3 = OPLS )
Element charge sigma (nm) epsilon (kJ/mol)
. . . .
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Specie residue name
Number of 1-4 pairs potentials
atom1 atom2 ScaleFactor
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Number of bonds
atom1 atom2 bond0 (nm) kbond (kJ/mol.nm²)
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Number of angles
atom1 atom2 atom3 ang0 (degs.) kang (kJ/mol.rad²)
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Dihedral angle potential type ('none', 'cos', 'harm', 'hcos', 'cos3', 'ryck', 'opls')
Number of dihedral angles
atom1 atom2 atom3 atom4 dihed_constants dihed_constants (depends on what is the potential)
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%