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MCCCS Towhee (input_style 'nucleic acid builder')

 

 

This section describes the input variables associated with an input_style setting of 'nucleic acid builder'. Uses the nucleic acid builder functionallity to set up everything for DNA or RNA from a list of the nucleic acids. Documentation of the currently available monomers is presented along with the forcefield information for each force field.

 

nunit (integer)
  • The number of monomers in this molecule. Must be less than or equal to NUMAX (see preproc.h) and there is also a check in the builder to make sure you do not exceed NUMAX with the number of atoms that all of your monomers require.
nmaxcbmc (integer)
  • The nmaxcbmc variable determines the largest number of atoms that are regrown during a configurational-bias regrowth. Since we only know the number of amino acids at this stage, and not the number of atoms, the final value of nmaxcbmc is computed as the product of the final number of atoms in the molecule times the input value of nmaxcbmc divided by the input value of nunit.
terminus (integer)
  • 3: the 3 prime end is terminated in a hydrogen and the 5 prime end has a phosphate group.
  • 5: the 5 prime end is terminated in a hydrogen and the 3 prime end has a phosphate group.
forcefield (character)
  • The forcefield that you want to use to build this molecule.
monomername (character)
  • Two letter code for the building blocks of the molecule. The monomernames can be found in the documentation for the appropriate forcefields for use with nucleic acid simulations. The monomers are listed in order (one per line) starting from the 5 prime end.
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Send comments to: Marcus G. Martin

Last updated: July 25, 2014