Check of Data and Initial Structure and Determination of Weights

This procedure checks the initial $R$ value and determines the ideal weight $W_A$ (and $W_P$ if a phase restraint is used) between $E_{XREF}$ and $E_{EMPIRICAL}$. The procedure should be carried out before running any refinement on the system. The weight $W_A$ is determined by running a brief molecular dynamics calculation without $E_{XREF}$ and then comparing the norm of the gradient of $E_{EMPIRICAL}$ and the norm of the gradient of $E_{XREF}$. The program will display the weight. A similar procedure should be applied when using targets other than the crystallographic residual (Eq. 13.1).

check.inp

If the minimizer exits with ``line search abandoned" and very large van der Waals energies (in the thousands of kcal mole$^{-1}$ ), the structure probably has bad contacts. The output of X-PLOR provides a list of bad contacts . One should check the molecule and symmetry-related molecules on the graphics and fix the problem. If this is inconvenient, try the following procedure: use the ``repel" nonbonded energy function (see Section 4.1) for the first several steps of minimization. One should replace the minimization statement in the example above with the following statements:

 parameter nbonds repel=0.89 rcon=4. end end  
                                             {*This turns on the repulsive *}
                                             {*function.                   *}
 minimize powell 
   nstep=40 
   drop=40.0 
 end 
                       {* This switches back to the Lennard-Jones function.*}
 parameter nbonds repel=0.0 end end 
 
 minimize powell                              
   nstep=40 
   drop=40.0 
 end