In version 31 a major restructuring of the topology and parameter
files was undertaken. This was performed to create a more modular
approach to the files, thereby avoiding the problem of files becoming
increasingly large.  The restructuring was done such that the primary
topology and parameter files for biomolecules can be used as they were
previously.  However, the topology and parameter information for the
majority of model compounds used in the parameter development,
additional molecules, including coenzymes, and patches parametrized to
be compatible with the CHARMM force fields have been moved to toppar
stream files.  These toppar stream files have to be streamed in a
CHARMM input script typically following reading of the parent topology
and parameter files.  They include both the topology and parameter
information for the selected molecules, using the "read rtf card
append" and "read param card append" commands to append the additional
information to the topology and parameter lists.  As of version c31 it
is still necessary to maintain all the MASS atom lists in the parent
topology and parameter files.

Topology files
 (1)  top_all22_prot.inp       all hydrogen RTF for proteins, CHARMM22
 (2)  top_all22_prot_cmap.inp  all hydrogen RTF for proteins, CHARMM22 with CMAP
 (3)  top_all22_sugar.inp      all hydrogen RTF for sugars
 (4)  top_all27_na.rtf         all hydrogen RTF for nucleic acids
 (5)  top_all27_lipid.rtf      all hydrogen RTF for lipids
 (6)  top_all27_na_lipid.rtf   all hydrogen RTF for nucleic acids and lipids
 (7)  top_all27_prot_na.rtf    all hydrogen RTF for proteins and nucleic acids
 (8)  top_all27_prot_lipid.rtf all hydrogen RTF for proteins and lipids
 (9)  toph19.inp               extended atom RTF for proteins
 (10) toprna10r_22.inp         extended atom RTF for nucleic acids

Parameter files
 (1)  par_all22_prot.inp       all hydrogen parameters for proteins
 (2)  par_all22_prot_cmap.inp  all hydrogen parameters for proteins with CMAP
 (3)  par_all22_sugar.inp      all hydrogen parameters for sugars
 (4)  par_all27_na.prm         all hydrogen parameters for nucleic acids
 (5)  par_all27_lipid.prm      all hydrogen parameters for lipids
 (6)  par_all27_na_lipid.prm   all hydrogen parameters for nucleic acids and lipids
 (7)  par_all27_prot_na.prm    all hydrogen parameters for proteins and nucleic acids
 (8)  par_all27_prot_lipid.prm all hydrogen parameters for proteins and lipids
 (9)  param19.inp              extended atom parameters for proteins
 (10) pardna10_22.inp          extended atom parameters for nucleic acids

(C) Toppar stream files (see stream subdirectory) listed under the parent 
topology and parameter files required for the individual files.

Parent files: can be used with prot, na and lipid files

 toppar_dum_nobel_gases.str: dummy atom, helium and neon
 toppar_hbond.str: stream file to estimate hydrogen bond interactions


Parent files: top_all22_prot.inp, par_all22_prot.inp
          (or top_all22_prot_cmap.inp, par_all22_prot_cmap.inp)

 toppar_all22_prot_model.str: model compounds used in protein parameter development
                              as well as additional compounds
 toppar_all22_prot_aldehydes.str: small molecule aldehydes
 toppar_all22_prot_aliphatic_c27.str: extends all22 protein force field to include
                              all27 alkane parameters        
 toppar_all22_prot_fluoro_alkanes.str: optimized fluoroalkanes, requires
                              toppar_all22_prot_aliphatic_c27.str
 toppar_all22_prot_heme.str: heme, O2, CO, CO2 and related patches
 toppar_all22_prot_pyridines.str: various substituted pyridines


Parent files: top_all27_na.rtf, par_all27_na.prm

 toppar_all27_na_model.str: model compounds used in na parameter development including
                              individual bases etc.
 toppar_all27_na_base_modifications.str: various chemical modifications of bases including
                              inosine
 toppar_all27_na_bkb_modifications.str: various chemical modificaiton of the na backbone
                              including abasic variants and phosphoramidate
 toppar_all27_na_carbocyclic.str: constrained bicyclic sugars
 toppar_all27_na_nad_ppi.str: NAD, NADH, ADP, ATP and others.  Useful in combination with
                              protein force field via the top_all27_prot_na.rtf
                              and par_all27_prot_na.prm


Parent files: top_all27_lipid.rtf, par_all27_lipid.prm

 toppar_all27_lipid_model.str: model compounds used in lipid parameter development, including
                               alkenes
 toppar_all27_lipid_cholesterol.str: cholesterol and related model compounds

Parent files: top_all27_prot_na.rtf, par_all27_prot_na.prm

 toppar_prot_na_all.str: all compounds that require both protein and nucleic acid toppar information
                              includes phosphorylated tyrosine, serine and threonine and some
                              coenzymes (SAH)

Parent files not needed

 toppar_water_ions.str: contains TIP3P water model and ions.  All of these
                              are also included in the prot, na and lipid topology
                              and parameter files.
 toppar_amines.str: highly optimized neutral aliphatic amines.


References: see doc/parmfile.doc or individual files
