Files “" and “" for Crystallographic Refinement (Polar Hydrogens)

This force field was developed by Engh and Huber (1991). It is a replacement for the “" and “" files that were used in previous versions of X-PLOR. Inconsistencies for a number of residues have been removed, which results in improved geometry and $R$ values. The energy constants were derived from observed uncertainties in geometric parameters obtained from the Cambridge Crystallographic Database for small model compounds. This file also contains patches to change the protonation degree of histidine residues (see also Section 3.8.4). The peptide-bond linkages (Section 3.7.3) are defined in “toph19.pep".

It was necessary to modify a number of improper and dihedral parameters compared to the “" and “" files. The twofold dihedral angle term for peptide bonds was replaced by a onefold term with a large energy constant. When using the original twofold term, transitions of peptide bonds from trans to cis conformations occurred at high simulated annealing temperatures. In the case of X-Pro peptide bonds, the twofold term was retained, but with an increased energy constant. To facilitate transitions between trans and cis prolines, the user should lower this energy constant with the atom-based parameter statement:

   dihedral ( name CA and resname * ) ( name C and resname * )  
            ( name N and resname PRO ) ( name CA and resname PRO )
            5. 2 180. 
The energy constants of the improper torsion angle that specify the chirality of $C^{\alpha}$ carbon atoms were also increased. The energy constants of the improper torsion angles that specify the planarity of aromatic rings were increased. In addition, the 1-4 and 1-5 nonbonded interactions in aromatic rings were included in the calculation. Without the increased energy constants and the nonbonded interactions, aromatic rings collapsed in a few cases where the initial coordinates contained bad contacts or large strain.

For crystallographic refinement, it is reasonable to reduce or delete the charges on charged residues, such as Lys, Arg, or Glu. To modify the charges, one can use the vector statement (Section 2.16); e.g.,

vector do ( charge=0.0 ) ( resname LYS and 
    ( name ce or name nz or name hz* ) )       {* Turn off charges for LYS.*}
vector do ( charge=0.0 ) ( resname GLU and
    ( name cg or name cd or name oe* ) )       {* Turn off charges for GLU.*}
vector do ( charge=0.0 ) ( resname ASP and
    ( name cb or name cg or name od* ) )       {* Turn off charges for ASP.*}
vector do ( charge=0.0 ) ( resname ARG and
    ( name cd or name *E or name cz or name NH* or name HH* )

Xplor-NIH 2023-11-10