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The structures found from systematic sampling are then energy minimized using either SYBYL's MAXIMIN2 facility ("Minimize" function of the "Compute" menu), MOPAC, or AMPAC.
The starting conformations can be automatically submitted to MAXIMIN2 using a 
that takes its input from a spreadsheet file and outputs the minimized conformations to a SYBYL database file. The SYBYL script can filter duplicate minimum energy conformations based on superposition and comparison. You must modify the script to correspond to the specific atom numbering scheme in your molecule.
Alternatively, energy minimization can be performed using MOPAC or AMPAC. The starting conformations can be obtained directly from systematic sampling or from molecular mechanics energy minimization, as previously described. A vectorized version of MOPAC 6.0 is currently available on the NIH Convex. The input for MOPAC 6.0 can be generated by SYBYL using a . You can modify the script to contain any desired MOPAC key words. All of the starting conformations must be loaded into SYBYL's molecule areas before running the script. The MOPAC input consists of a ".dat" file for each starting conformation.
When the script has completed, you must "ftp" (see the Unix "man ftp" command for information) the ".dat" files from your workstation to the Convex. The output from MOPAC 6.0 consists of one ".arc" and one ".out" file for each minimum energy conformation. The MOPAC ".out" files summarize the minimization steps, together with any error messages concerning convergence. Next, "ftp" all of the ".arc" files of properly converged minima back to your workstation, and run to retrieve the results into a SYBYL molecule database.
Duplicate minimum energy conformations, whether obtained using MAXIMIN2 or MOPAC, can be filtered using a .