
Changes in the CHARMM toppar file format.
updated July 2015

As of July 2015 a new, additional version of the topology and
parameter files has been created in which the MASS numbers are all set
to -1.  This coincides with changes in version 39 of CHARMM and onward
in which the MASS numbers are assigned as the new atom types are read.
This avoid problems with overlapping mass numbers, which has become an
issue as we have increased the number of atom types with CGenFF as
well as other aspects of the force field.  As of July 2015 the default
version of the toppar files will contain the traditional MASS numbers
with a second version of the files included with "MASS -1".  This will
allow for earlier versions of CHARMM to be used.  As of July 2016 we
anticipate moving to "MASS -1" as the default for all the toppar
files.

!July 2013

To facilitate the application of the CHARMM force field to
heterogeneous systems the toppar files have been converted to a
self-contained "stream" file format.  This allows for each of the
individual sets of toppar files to be read in consequtively for
complex systems.  For example, for a protein-inhibitor complex, the
protein topology and parameter files would be read followed by the
CGenFF topology and parameter files.  To perform this the append and
flexible parameter reader are used, as shown below.  Note that this
approach requires that the water and ion toppar files be read in
explicitly as they are no longer included in any of the parent toppar
files. To allow this approach the MASS numbers in each of the sets of
toppar files is unique as required to read them individually.  The
range of MASS numbers in the individual files is given below. Note
that this file format has been tested on versions c34, c35 and c36 of
CHARMM; however it should work on version c32 and all subsequent
versions.

Another significant change is in the terminal patching in the nucleic
acids. See the top_all36_na.rtf for details.

Reordering of atoms in PC (choline) containing lipids as required for
new domain decomposition code in CHARMM

Summary of toppar files

toppar_water_ions.str: contains TIP3 water model and ion topology and
parameter information.  This is now the only file that contains these
entities.

Toplogy files
top_all22_prot.rtf    all atom additive RTF for proteins, CHARMM22 with CMAP
top_all36_prot.rtf    all atom additive RTF for proteins, CHARMM36 version, July 2012
top_all36_na.rtf      all atom additive RTF for nucleic acids, RNA/DNA updates
top_all35_ethers.rtf  all atom additive RTF for ethers
top_all36_carb.rtf    all atom additive RTF for carbohydrates
top_all36_cgenff.rtf  all atom additive	RTF for general molecules
top_all36_lipid.rtf   all atom additive	RTF for lipids
toph19.inp            extended atom RTF for proteins

Parameter files
par_all22_prot.prm    all atom additive parameter for proteins, C22 with CMAP
par_all36_prot.prm    all atom additive parameter for proteins, CHARMM36 version, July 2012
par_all36_na.prm      all atom additive	parameter for nucleic acids, RNA/DNA updates
par_all35_ethers.prm  all atom additive	parameter for ethers
par_all36_carb.prm    all atom additive	parameter for carbohydrates
par_all36_cgenff.prm  all atom additive	parameter for general molecules
par_all36_lipid.prm   all atom additive	parameter for lipids
param19.inp           extended atom parameters for proteins

stream subdirecties: contain various molecules that have been
parametrized in the context of the CHARMM additive force fields. These
files require the specific "parent" toppar files be read prior to
reading these files. The dependencies are indicated in the individual
files.

stream/prot

toppar_all36_prot_aldehydes.str        small molecule aldehydes
toppar_all36_prot_arg0.str             neutral arginine model compounds and patches
toppar_all36_prot_d_amino_acids.str    d-amino acids with the c36 protein force field
toppar_all36_prot_fluoro_alkanes.str   optimized fluoroalkanes, requires 
                                       toppar_all22_prot_aliphatic_c27.str
toppar_all36_prot_heme.str             heme, O2, CO, CO2 and related patches
toppar_all36_prot_model.str            model compounds used in protein parameter 
                                       development as well as additional compounds
toppar_all36_prot_modify_res.str       various modifed amino acid residues/patches
                                       include posttranslational modifications (see na combined)
toppar_all36_prot_na_combined.str      residues and patches, including phosphotyrosine, 
                                       serine and threonine that require both protein and
                                       nucleic acid toppar parent files.
toppar_all36_prot_pyridines.str        various substituted pyridines
toppar_all36_prot_retinol.str          retinol, model compounds, Schiff's bases

stream/na

toppar_all36_na_modifications.str      various chemical modifications of bases, backbone
                                       and sugars (including carbocyclic sugars)
toppar_all36_na_model.str              model compounds used in na parameter development
                                       including individual bases etc.
toppar_all36_na_nad_ppi.str            NAD, NADH, ADP, ATP and others.  
toppar_all36_na_reactive_rna.str       reactive species associated with phophate hydrolysis
toppar_all36_na_rna_modified.str       modified RNA nucleotides (as in tRNA etc.)

stream/lipid

toppar_all36_lipid_bacterial.str      various lipids found in bacteria
toppar_all36_lipid_cardiolipin.str    cardiolipin
toppar_all36_lipid_cholesterol.str    cholesterol; note that old cholesterol used on Anton
toppar_all36_lipid_detergent.str      various detergents
toppar_all36_lipid_glycolipid.str     various glycolipids
toppar_all36_lipid_inositol.str       lipids contain various inositol analogs
toppar_all36_lipid_list.str           list of required files for running test cases
toppar_all36_lipid_llo.str            lipid linked oligosaccharides
toppar_all36_lipid_miscellaneous.str  various lipids
toppar_all36_lipid_model.str          model compounds used in lipid parameter development
toppar_all36_lipid_prot.str           protein residues modified with lipids
toppar_all36_lipid_sphingo.str        Ceramide/sphingomylein
toppar_all36_lipid_yeast.str          various lipids in yeast

stream/carb

toppar_all36_carb_glycolipid.str       model compounds for glycolipids
                                       (some overlap with stream/lipid contents)
toppar_all36_carb_glycopeptide.str     model compounds for glycoproteins
toppar_all36_carb_model.str            model compounds using in carbohydrate parameter development

stream/misc

toppar_amines.str                      highly optimized neutral aliphatic amines
toppar_dum_noble_gases.str             nobel gases and dummy atom
toppar_hbond.str                       stream file to estimate hydrogen bond interactions
toppar_ions_won.str                    extensive collection of ion parameters that covers
                                       the majority of the periodic table.  Caution: use
                                       optimized ions in toppar_water_ions.str when possible.

(D) Parameters for the polarizable force field based on a classical
Drude oscillator.  As this force field is currently under development
such that the parameters have been placed in the "drude" subdirectory.
It is suggested that these be obtained from the MacKerell lab force
field web page.  Also accessible via the CHARMM Gui.  See the 00readme
for details and the approriate references.

(E) Parameters for selected silicate and aluminosilicate surfaces have
been developed.  These parameters are designed to be compatible with
the CHARMM22, 27 and 36 force fields allowing for biological
molecule-silicate surface interactions.  As use of these parameters
requires creation of the surface, which entails creation of the
necessary patches, the parameters are included in the "silicates"
subdirectory.  This directory also includes examples and code to
create the extended surfaces. See the 00readme file for more details.

ref: Lopes, P.E.M., Murashov, V. Tazi, M. Demchuk, E. MacKerell,
A. D., Jr. "Development of an Empirical Force Field for
Silica. Application to the Quartz-Water Interface," Journal of
Physical Chemistry B, 110: 2782-2792, 2006.

(F) Additional topology and parameter files from various sources are
included in subdirectories of the toppar directory.  A description
follows:

subdirectory non_charmm: Contains toppar files for AMBER,
Bristol-Myers Squibb (BMS) and OPLS force fields along with stream
files for a variety of water models.  These files have been tested
to the extent that they may be considered reliable representations of
the original force fields, though potentially not exact
representations.  These files are NOT maintained and, thus, use at
your own risk.  See the 00readme files and note that AMBER requires a
special version of CHARMM as described in the 00readme file.

tamdfff: An internal coordinate force field (ICFF) that was built
based on the CHARMM 22 protein force field.  Specifically, it provides
a backbone covalent geometry suitable for torsion angle molecular
dynamics (TAMD) and the necessary CMAP cross-term corrections to
suppress distortions of the potential energy surface due to rigid
covalent geometry.  Additional details can be found in tamd.doc.

Ref. J. Chen, W. Im and C. L. Brooks III, J. Comp. Chem. 2005, 26,
1565-1578.

rush: A simple implicit-solvent protein force-field that adds terms to
the bonded portion (bond + angle + dihe + impr + urey) of the all-atom
CHARMM22 force field to account for volume-exclusion (_R_epulsion),
the hydrophobic effect (_U_nburied _S_urface), and intra-molecular and
protein-solvent hydrogen-bonding (_H_ydrogen-bonding) (hence _R_ _U_
_S_ _H_).  Usage instructions are in doc/rush.doc

gbsw: Optimized protein backbone parameters (par_all22_prot_gbsw.inp)
and atomic input radii (radius_gbsw.str) for a balanced GBSW implicit
solvent force field.  The backbone phi/psi cross-term (CMAP) and the
atomic input radii have been re-optimized specifically to balance the
solvation and intramolecular interactions and to capture experimental
conformational equilibria of both helical peptides and
beta-hairpins. Additional information can be found in gbsw.doc.

Ref. J. Chen, W. Im and C. L. Brooks III, J. Am. Chem. Soc.  128,
3728-36 (2006).

ace: ACE2 solvation model developed by Michael Schaefer

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

Example of command to read protein, nucleic acid and water/ions in a
CHARMM script

*  Generate and energy of molecules that require a combined
*  Example to read protein, nucleic acid and water/ion toppar information
*

set dir !set toppar directory

set a @dir/top_all36_prot.rtf
set b @dir/par_all36_prot.prm
set c @dir/top_all36_na.rtf
set d @dir/par_all36_na.prm
set e @dir/toppar_water_ions.str

! read the protein topology
read rtf card name @a

! read the protein parameters
read para card flex name @b 

! append the nucleic acid topology
read rtf card append name @c 

! append the nucleic acid parameters
read para card flex append name @

! append water and ion toppar information
stream @e

!remainder of charmm script.......

stop

>>>>>>>>>>>>>>>>>>>>>>>>>>
TOPPAR file MASS numbering

Parent toppar files

Water and ions: MASSes 1 to 20
toppar_water_ions.str

Proteins: MASSes 41 to 90
top_all36_prot.rtf
par_all36_prot.prm

Nucleic acids: MASSes 91 to 135
top_all36_na.rtf
par_all36_na.prm

Lipids: MASSes 136 to 170: 165-168 in toppar_all36_lipid_cer2.str
top_all36_lipid.rtf
par_all36_lipid.prm

Carbohydrates: MASSes 171 to 230
top_all36_carb.rtf
par_all36_carb.prm

Ethers: MASSes 241 to 260
top_all35_ethers.rtf
par_all35_ethers.prm

CGenFF: MASSes 256 to 400
top_all36_cgenff.rtf
par_all36_cgenff.prm


>>> Stream files subdirectory stream: Only those stream files that
contain novel atom types are listed below.

toppar_all36_prot_aldehydes.str:        MASSes 418

toppar_all36_na_modifications.str:      MASSes 416 to 417, 469 to 483

toppar_all36_prot_pyridines.str:        MASSes 419 to 424

toppar_all36_prot_retinol.str:          MASSes 425 to 429

toppar_all36_prot_fluoro_alkanes.str:   MASSes 430 to 437

toppar_all36_prot_d_amino_acids.str     MASSes 438, 439

toppar_amines.str:                      MASSes 446 to 458

toppar_all36_na_nad_ppi.str:            MASSes 459 to 465

toppar_all36_na_model.str:              MASSes 466 to 468

toppar_all36_prot_na_combined.str:      MASSes 484 to 485

toppar_all36_prot_heme.str:             MASSes 486 to 494

toppar_dum_nobel_gases.str:             MASSes 495 to 499

toppar_all36_prot_arg0.str              MASSes 501 to 509

toppar_all36_na_reactive_rna.str        MASSes 510 to 521

toppar_all36_lipid_cer2.str             MASSes 165 to 168
