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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 ) endEffective energy term databases may also need some modification; e.g., the crystallographic database should be modified to select only known atoms:
xrefin selection=( known ) endNote 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 2024-09-13