Topology and parameter file generation

Gerard 'CD' Kleywegt GERARD at XRAY.BMC.UU.SE
Wed Nov 22 13:13:57 EST 1995


For those of you who have been using XPLO2D to generate
X-PLOR topology and parameter files, there is a new
version with three improvements:

- DIHEdral statements are now included in the parameter file

- you may use the occupancy column of your input PDB file to
  contain the number of (implicit) hydrogen atoms for every heavy
  atom.  This will help the program in finding out which atoms
  are equivalent.  As a bonus, the MASS statements for C, N, O
  and S atom types will contain the correct masses

- you may help the program even more by using the B-factor column
  of your input PDB file to contain a flag (must be a near-
  integer number) which is equal for equivalent atoms.  In this
  way you decide which atoms are equivalent, rather than the
  program.  As always: garbage-in, garbage-out - the program
  trusts you blindly, so if you say that a carbon and an
  oxygen atom are equivalent, that's what you'll get.  In general,
  I would first switch this option off to see what the program
  thinks are equivalent atoms.  It is easy to overlook equivalences
  (and subtle differences) !  If the program's conceptions don't
  agree with your own, you can enforce them using this new option

The latest version can be ftp-ed from rigel.bmc.uu.se,
directory pub/heteros (O users can download it from the
O ftp server as well).

--Gerard



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