How the Type-based Parameter Retrieval Works

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How the Type-based Parameter Retrieval Works

This example shows how X-PLOR finds parameters for the covalent bonds, bond angles, improper angles, and nonbonded energy terms. It demonstrates that the introduction of atom types greatly reduces the number of parameters that have to be specified. The parameter retrieval is carried out when the energy statement is issued.

topology 
   residue test
   atom a1  type=b  end
   atom a2  type=b  end
   atom a3  type=b  end
   atom a4  type=a  end
   atom a5  type=a  end
   atom a6  type=a  end

   bond a6    a5
   bond a5    a4
   bond a4    a2
   bond a4    a3   
   bond a4    a1   

   angle a6 a5 a4                     {* One could have saved work here by *} 
   angle a5 a4 a3                     {* using the autogenerate option.    *}
   angle a5 a4 a2
   angle a5 a4 a1
   angle a1 a4 a3
   angle a1 a4 a2
   angle a2 a4 a3

   dihedral a6 a5 a4 a3
   dihedral a6 a5 a4 a2
   dihedral a6 a5 a4 a1

   improper a1 a2 a3 a4
   end
end 

parameter
   bond a  b  100.0       1.0
   bond a  a  100.0       1.0
   angle a  a  a   50.0  100.0 
   angle b  a  b   50.0  100.0 
   angle a  a  b   50.0  100.0 
   dihedral a  a  a  b   80.0  3 0.0
   improper b  b  b  a   30.0  0 180.0
   nonbonded a 0.1 1.0 0.1 1.0
   nonbonded b 0.1 1.0 0.1 1.0
end 

segment
  name=test
  molecule number=1 name=test end
end

energy end

Xplor-NIH 2024-09-13