Van der Waals radii

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Van der Waals radii

The $\sigma$ values (cf. Eqs. 4.8 and 4.10) in the parameter file “parallhdg.pro" are different from those used in the other all-hydrogen force fields. The changes were made to make the van der Waals radii more consistent with those used by other NMR refinement programs. The $\sigma$ values have been set such that the van der Waals radii will be exactly like those used by the DISGEO program (Havel and Wüthrich, 1984) when REPEl (Section 3.2.1) is set to 0.8. In addition, van der Waals radii of potential hydrogen bond donor-acceptor pairs have been reduced by appropriate NBFIx statements. The actual van der Waals radii used for different values of REPEl are given in the table below (in Å).

type	repel=1.0	repel=0.9	repel=0.8	repel=0.75
H	1.250	1.125	1.0	0.938
C	1.875	1.688	1.5	1.406
N	1.688	1.519	1.350	1.266
O	1.558	1.402	1.246	1.168
S	2.102	1.892	1.682	1.577

It should be noted that the van der Waals radii in “parallhdg.pro" are not appropriate with the standard Lennard-Jones potential (Eq. 4.8).

Xplor-NIH 2025-03-21