Check of Data and Initial Structure and Determination of Weights

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Check of Data and Initial Structure and Determination of Weights

This procedure checks the initial

value and determines the ideal weight

(and

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

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

Xplor-NIH 2025-11-07