prep file

Data from: http://ambermd.org/doc/prep.html

It is not necessary to run PREP if all residues needed for a simulation  are  already  present in the standard  AMBER  database, described in the LINK documentation.

Dummy atoms: PREP requires that three dummy atoms  precede
the  actual  atoms of the residue.  These atoms are simply used
to define the space axes for  the  residue.   The  three  dummy
atoms  must be given the topological type "M", and they must be
assigned a force field atom type that defines them   as   dummy
atoms.   The   symbol   "DU"   is  recommended to be consistent
with the standard database.   It  is  necessary  to  have   the
three  initial   dummy   atoms   whether  internal or cartesian
coordinates are given as input.

A 4° coluna pode ser representada por  "Main", "Side", "Branch", "3", "4", "5" "6" e "End" tipos..
Observe que E (end) são os átomos que possui apenas uma ligação, como neste caso são os átomos de hidrogênio.