2.6 Adding New Residue Types

If HBPLUS does not recognise an atom, or a residue, it will issue a warning
statement.  For instance "WARNING: Residue SO4 is not recognized by HBPLUS".
If one of the unrecognised atoms has an role in hydrogen bonding - for
instance it is a donor or acceptor, or connected to a donor or acceptor,
you will probably want to define the residue or atoms within HBPLUS.

This requires the five command line options -U/u (new residUe, with or
without a similar old residue), -M (new atoM), -T (connecT) and -e/E (new
donor/acceptor).  You will probably find it wise to use the -f option and
place the additional information in a separate file.  The syntax for these
commands is quite important.  Residue names are always three characters
long, and atom names are always four.  If neccessary, use quotes to make
the presence of trailing spaces obvious.  Each bond in the list of bonds
given to the -T command is in the form of two four-letter atom code with
each bond terminated by a colon.

For instance

#HBPLUS option file to add SO4 residue
-u SO4 #name the residue
-M SO4 " S  " #first atom
-M SO4 " O1  O2  O3  O4 " #more atoms
-T SO4 " S   O1 : S   O2 : S   O3 : S   O4 :" #the bonds
-e SO4 " O1 " 2 #each oxygen can accept two H-bonds
-e SO4 " O2 " 2
-e SO4 " O3 " 2
-e SO4 " O4 " 2

If the new residue is similar to one of the old residues and the atoms bear
the same four-letter names, then the '-U' option can be used and the other
atoms and covalent bonds added.

For instance

#HBPLUS option file to add NADP+ residue, called NAP
-U NAP NAD                         #Similar structure and atom names to NAD
-M NAP "AP2*AOP1AOP2AOP3"           #the new phosphate group
-T NAP "AP2*AOP1:AP2*AOP2:AP2*AOP3:" #Covalent bonds within the phosphate
-T NAP "AO2*AP2*:"                   #Covalent bond to the phosphate
-e NAP "AOP1" 2                      #each oxygen can accept two H-bonds
-e NAP "AOP2" 2
-e NAP "AOP3" 2