#!/bin/csh
#
# adds protons to a PDB file and converts names to amber format
# suffix is changed to .apdb
# usage pdb2amber pdb_file(s)
#
foreach file (f36g_1d???.pdb)
   protonate -d PROTON_INFO < $file | sed -e 's/\ H1\ /\ H\ \ /g' -e '/\ H2\ /d' -e '/\ H3\ /d' | pdb_renumber > $file:r.apdb 
end