modified on 18 February 2011 at 15:38 ••• 14,965 views

Qmmm example9

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Example of QM/MM frequency calculation for classical region

This example illustrates QM/MM frequency calculation for Ala-Ser-Ala system. In this case instead of default QM region (see prepare block), the calculation is performed on classical solute part of the system as defined by region directive in QM/MM block. The electrostatic field from fixed QM region is represented by point ESP charges (see density directive). These ESP charges are calculated from wavefunction generated as a result of energy calculation.

 memory total 800 Mb

 start asa

 permanent_dir ./perm
 scratch_dir ./data

 #this will generate topology file (asa.top), restart (asa_ref.rst), and pdb (asa_ref.pdb) files.
 prepare
   source asa.pdb
   new_top new_seq
   new_rst
   modify atom 2:_CB quantum
   modify atom 2:2HB quantum
   modify atom 2:3HB quantum
   modify atom 2:_OG quantum
   modify atom 2:_HG quantum
   center
   orient
   solvate
   update lists
   ignore
   write asa_ref.rst
   write asa_ref.pdb   # Write out PDB file to check structure
 end
 task prepare

 md
   system asa_ref
 end

 basis "ao basis"
   * library "6-31G*"
 end

 dft
  print low
  iterations 500
 end

 qmmm
 region mm_solute
 density espfit
 end

 # run energy calculation to generate wavefunction file for subsequent ESP charge generation
 task qmmm dft energy
 task qmmm dft freq