Examples of Atom-based Modifications of the Parameters

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Examples of Atom-based Modifications of the Parameters

The first example shows how to set the energy constants of all improper angles involving tyrosine residues to 500 kcal mol $^{-1}$ rad $^{-2}$ . The periodicity and the equilibrium constants are untouched by the TOKEn keyword.

parameter
   improper ( resname tyr ) ( resname tyr ) 
            ( resname tyr ) ( resname tyr )  500 TOKEN TOKEN
end

In the next example, the energy constants of all bonds are set to 400 kcal mole $^{-2}$ Å $^{-2}$ :

parameter 
   bond ( all ) ( all ) 400. TOKEN
end

In the next example, the energy constant for the $\omega$ torsion angle for X-Pro peptide bonds is set to 500 kcal mole $^{-1}$ Å $^{-2}$ . This example applies only to parameter files that define the $\omega$ torsion angle as a dihedral angle, such as “toph19.pro" or “tophcsdx.pro".

parameter
   dihedral ( name CA and resname * ) ( name C and resname * ) 
            ( name N and resname PRO ) ( name CA and resname PRO )
            500 TOKEN TOKEN
end

The last example is similar to the previous one, except that, in addition to increasing the energy constant, the periodicity is set to one and the equilibrium angle is set to 0 $^{\circ}$ ; i.e., only trans prolines are allowed.

parameter
   dihedral ( name CA and resname * ) ( name C and resname * )  
            ( name N and resname PRO ) ( name CA and resname PRO )
            500 1 0. 
end

Xplor-NIH 2025-03-21