Getting started - Your Own Main Table of Contents

VERSION 4.0 Sun 18 Jan 2009

Your own System

For proteins in water (or other solvent) the route is described above. For other systemd (eg. pure liquids or mixtures) one needs:

• The atomic coordinates, which can be generated by a variety of interactive programs (eg. Quanta, Cerius, HyperChem). Coordinate files can be exported in pdb-format and converted to .gro format by the editconf program:
  
  

  editconf -f conf.pdb -o conf.gro

  
  where conf.gro is the coordinatefile, or converted back to pdb-format by
  
  

  editconf -f conf.gro -o conf.pdb

  
  where conf is a file with coordinates, and conf.pdb is the target file in .pdb format. NOTE: Make sure that the graphics programs export whole molecules instead of molecules that are cut in pieces (due to the periodic boundary conditions) If you have the coordinates of single molecules, you can also build systems (pure liquids or mixtures) with genbox. In contrast, the program genconf produces the lattice of molecules with random displacements.
• The topology you have to build yourself. Of course you can include topologies of part of your system (eg. spc.itp, decane.itp etc.)