newhyd - inserts protons into a PDB heavy atom file

SYNOPSIS
     newhyd

DESCRIPTION
     newhyd takes a PDB file and attaches  protons  according  to
     hybridization  and  connectivity  information contained in a
     pair of database files.  Protons are  given  rational  four-
     character names according to the rules:

          Carbon protons are named H/remoteness/branch/sequence:

                   CA, CB, CG1     ->   HA, HB1, HB2, HG11, HG12

          Heteroatom protons are H/hetatm/remote/sequence:

                    NA, NB    ->   HNA, HNB1, HNB2

          or if necessary: H/hetatm/branch/sequence:
              NH1  ->   HN11, HN12

     The program queries the user if all protons are to  be  gen-
     erated, or if only nonexchangeable protons are wanted.  Then
     it prompts the user for the input  file  name,  output  file
     name,  and whether the default database files are to be used
     for connectivities and hybridization.  The user can  specify
     alternate  radii  and  hybrid  files which should follow the
     format of the standard database files.  The hybrid  database
     currently  contains information for 20 standard amino acids,
     the nucleic acids ADE, CYT, GUA, THY  and  URA.   Additional
     residues  can be added to the hybridization and connectivity
     database files if of general utility.

INPUT
     newhyd prompts for four files:

     Input file name:file.PDB
     Output file name:fileH.pdb
     Radii file:(the default can be accepted with a .)
     Hybridization file:(the default can be accepted with a .)
  You can specify your own radii and hybridization files which
     should  follow  the  format  of  the athyd.data and chem.con
     files.
FILES
     athyd.data     standard hybridization file
     chem.con  standard radii file


AUTHOR
     newhyd  is  a  modification  by  Brandan   Borgias   of   N.
     Pattabiraman's  program newfixhy, for generation of hydrogen
     coordinates from a PDB  format  coordinate  file.   Rational
     names  are generated for the protons.  Connectivity informa-
     tion is now generated  in  the  program  rather  than  being
     required as a seperate previous step.
 
     Brandan A. Borgias
     Department of Pharmaceutical Chemistry
     University of California--San Francisco
BUGS
     newhyd expects a file with only heavy atoms.   It  will  not
     strip  away  protons already in place and will not overwrite
     protons already present. Limited to 2000 atoms and 400 resi-
     dues.

     newhyd expects the N terminal Nitrogen atom to be  first  in
     the  list and will always protonate it with three protons in
     sp3 configuration.  If N is not atom  1,  then  it  will  be
     given  two  protons n sp2 configuration.  Users wishing neu-
     tral N-termini must delete the proton of their choice.