modified on 25 May 2012 at 12:08 ••• 1,472 views

Release62:Qmmm example asa prepare

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 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