
Index of toppar stream files that contain miscellaneous compounds
and patches that extended the charmm force field functionality
as well as containing the model compounds used in the force
field development.

These files are typically streamed into charmm following reading
of the appropriate topology and parameter files.  During the
streaming, the additional topology and parameter information for
the new molecules is read via the "read rtf append" and "read
param append" commands.

(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_all31_prot.rtf, par_all31_prot.prm)

 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
 toppar_all22_model_aliphatic.str: model compounds used in protein parameter development
                              but treated with all27 alkane parameters (not for general use)

Parent files: top_all27_na.rtf, par_all27_na.rtf

 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.rtf

Parent files: top_all27_lipid.rtf, par_all27_lipid.rtf

 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.rtf

 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.


