Residue Topology File
By Alexander D. MacKerell Jr., May 1991
This section of the documentation describes the contents of the
topology file and a listing of the current topology files available to
the users. CHARMM topology files contain the information necessary to
describe bond connectivity, angle, dihedral angle and improper
dihedral angle content, charge distribution, hydrogen-bond donors and
acceptors and internal coordinate information. Thess data are required
by CHARMM in order to determine energies, perform energy minimizations
and molecular dynamics simulations as well as perform other various
structural manipulations. Documentation concerning implementation of
a topology file in order to build a structure is contained in
STRUCT.DOC.
* Menu:
* Overview:: Overview of CHARMM Topology File
* RTFDATA:: Description of Topology Files available for general use
Overview of CHARMM Topology File
An example of a topology file is given below followed by
a description of the content of the various sections. Also see
IO.DOC for information on the individual keywords.
(A) * CHARMM example topology file
*
(B) 19 1
(C) MASS 1 H 1.00800
MASS 2 O 15.99900
(D) DECL -C
DECL -O
DECL +N
DECL +H
DECL +CA
(E) DEFA FIRS NTER LAST CTER
(F) AUTOGENERATE ANGLES DIHEDRAL
(G) RESI GLY 0.000
(G1) GROUP
(G2) ATOM N NH1 -0.35
ATOM H H 0.25
ATOM CA CH2E 0.10
GROU
ATOM C C 0.55
ATOM O O -0.55
(G3) BOND N CA CA C C +N C O N H
BOND CA CB
(G4) ANGL N CA C (and so on)
(G5) DIHE -C N CA C N CA C +N CA C +N +CA
(G6) IMPH N -C CA H
(G7) DONO H N
(G8) ACCE O C
(G9) IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000
IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000
IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000
IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000
IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000
IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000
(G10) PATCH FIRST NONE LAST NONE
(H) PRES CTER -1.000
(H1) DELE ATOM O
(H2) ATOM C C 0.14
ATOM OT1 OC -0.57
ATOM OT2 OC -0.57
(H3) BOND C OT1 C OT2
ANGL OT1 C OT2 (and so on)
DIHE N CA C OT2
IMPH C CA OT2 OT1
(H4) ACCE OT1 C
ACCE OT2 C
IC N CA C OT2 0.0 0.0 180.0 0.0 0.0
IC OT2 CA *C OT1 0.0 0.0 180.0 0.0 0.0
(I) END
The topology file starts with the title (A) which contains
information on the origins and applicability of that file. This is
followed by (B) the CHARMM version number under which that particular
file was developed.
Section (C) contains the various atom types used in the
topology file and is signified by the keyword MASS. Information
includes a number associated with each atom type, the atom type
followed by the mass of the atom. The number of each atom type is
used in conjunction with the parameter file (see PARMFILE.DOC) and is
the marker for the various energy term arrays (bonds, angles etc.)
Section (D), signified by DECLare, prescribes which atoms will
be selected from the previous or next residue when covalently linking
residue together as in the connection of residues in a polypeptide via
a peptide bond linkage.
Section (E) contains the DEFAult patches used on the FIRSt and
LAST residues in a generated segment (i.e. the NTERminus and CTERminus
of a polypeptide chain, see section (G10). (F) Next are the
AUTOgenerate default options to be used when building a sturcture.
AUTO ANGLes specifies that all possible angles and DIHEdral specifies
that all possible dihedral angles be generated when building a
structure. If these options are not included the angles and/or
dihedrals must be listed explicitly in the topology file (see G4 and G5).
Designation of the various residues, nucleotides etc. is done
using the (G) RESIdue keyword followed by the residue name (four
characters) and the total charge of the residue. A residue may then
be subdivided into (G1) GROUps, which contain several atoms whose total
charge is neutral or a unit charge. This subdivision is used in the
calculation of nonbonded interactions using the group keyword and in
the extended electrostatics options (see NBONDS.DOC). Next are the
individual ATOM specifications which include the IUPAC atom name, the
atom type and the charge of that atom. In certain cases 1 or more
atom names will follow the charge which indicate atoms which are to be
excluded from nonbond calculations with that particular atom (i.e.,
used to exclude atoms in rings from seeing each other in topologies
prior the CHARMM22 releases).
Following the various atoms are the (G3) BOND connectivites,
the (G4) ANGLe, the (G5) DIHEdral and (G6) IMPRoper dihedral listings.
The BOND are IMPRoper listings are always required while the ANGLe
and/or DIHEdral listings should be omitted if the AUTOgenerate ANGL
and/of DIHEdral options are being used. It should be remembered that
the autogeneration only works in conjunction with the GENErate
command; in PATChes invoked after the initial structure generation the
angles and dihedrals must listed explicitly.
For making hydrogen bond lists the (G7) DONOr and (G8) ACCEptors
must be listed. These listings include the donor and donor antecedent
and the acceptor and acceptor antecedent atom names. The antecedents
are required if hydrogen bond angle cutoffs are being invoked (see
HBONDS.DOC). If only the hydrogen bond distance criteria are desired,
as with the amber force field the antecedents should be omitted and
the BLNK inserted prior to the donor atom name (e.q. DONO BLNK H1 and
ACCE O2). Section (G9) contains the internal coordinate information
(IC or BILD) which may be used to build a molecule or add missing
atoms, such as hydrogens to a crystal structure (see IO.DOC and
INTCOR.DOC).
The next line (G10) contains the PATChes to the FIRSt and LAST
atoms of the residue and is required on when the DEFAult (E) is to
be overridden.
Along with RESIdues the topology also contains patch residues,
(H) PRES, which may be used at the termini of a structure, alter a
RESIdue structure or form covalent links between residues (e.g.
disulfide bridges). PRESidues may be used in either a GENErate or
PATCh statement (see STRUCT.DOC). In addition to the contents of the
standard RESIdue atoms may also be (H1) DELEted (see IO.DOC) from a
residue. Atoms already specified in the initial residue may be
respecified in order to change the atom type or CHARGE. The GROUp
option may also be included to alter the group lists. Again (H3) BOND
and IMPRoper listings must be included. The ANGLe and DIHEdral
listings only need to be included if the AUTOgenerate option is not
used OR if the PRES is used in a PATCh following the GENErate
statement. Finally, (H4) a PRES may specify new DONOrs and ACCEptors
and new IC or BILD statements.
Exiting the topology file is done with the (I) END command.
Description of Topology Files Available for general use
Currently topology files for both proteins and nucleic acids
exist using both all-hydrogen and extended atom representations. The
most recent topologies are the all-hydrogen sets for proteins,
TOP_ALL22_PROT.INP, and for nucleic acids, TOP_ALL22_NA.INP. The
extended atom protein, TOPH19.INP, and nucleic acid, TOPRNA10R_22.INP,
topologies are from the Version 19 release. Alterations in the
dihedrals have been made to TOPRNA10R_22.INP to reproduce the original
results, however, due to the small increase in the number of atoms
upon going from the extended to all-hydrogen representations in
nucleic acids it is recommeded that TOP_ALL22_NA.INP be used.
Hopefully, in the not to distant future, new extended atom topologies
will be developed based on the all-hydrogen files.
References for the all-hydrogen protein and nucleic acid
topology files are
Proteins:
MacKerell, A. D. Jr. et al., Manuscript in Preparation.
Nucleic Acids:
MacKerell, A. D. Jr., Wiorkiewicz, J. and Karplus, M., Manuscript
in Preparation.
It is anticipated that the above will be submitted in J. Am.
Chem. Soc. There will also be a series of papers on the
parameterization of various residue types.
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory