What to Do about Unknown Atoms

X-PLOR meticulously keeps track of unknown atomic positions and normally terminates execution if one wants to compute energies with unknown atoms. How to get around this? There is a simple answer: create appropriate positions with the graphics, or simply guess coordinates and let the minimizer take care of the geometry. If this is not possible, for instance in cases of disordered side-chain atoms, then the following procedures should be applied: in the molecular structure generation file, ignore the warning messages from the hydrogen builder regarding unknown heavy atom positions. In subsequent files, insert the following statement after reading the molecular structure file:
constraint interaction=( known ) ( known ) end
Effective energy term databases may also need some modification; e.g., the crystallographic database should be modified to select only known atoms:
  selection=( known ) 
Note that X-PLOR occasionally produces unknown atom positions when the molecular dynamics or energy minimization routines run into numerical instabilities. Usually, the energies become very large before this happens. It can occur because the temperature of the molecular dynamics calculation is too high, the time step is too large, or the conformation is extremely strained.

Xplor-NIH 2024-06-11