rtop (c40b1)
Residue Topology File
By Alexander D. MacKerell Jr., January 2008
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.
* Overview | Overview of CHARMM Topology File
* RTFDATA | Description of Topology Files available for general use
By Alexander D. MacKerell Jr., January 2008
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.
* Overview | Overview of CHARMM Topology File
* RTFDATA | Description of Topology Files available for general use
Top
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 H
MASS 2 O 15.99900 O
(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
DOUBLE CA CB
TRIPLE CB CG
(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) CMAP -C N CA C N CA C +N
(G8) DONO H N
(G9) ACCE O C
(G10) 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
(G11) 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
directly followed by (B) the CHARMM version number under which that
particular file was developed. Note that this must be on the line
directly following the title.
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 final column is the atomic type
and is included for compatibility with the MMFF code. 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 listings are always required in order to define the
connectivity of the molecule; BOND can be replaced by DOUBLE, TRIPLE
or AROMATIC allowing for compatibility with MMFF. The ANGLe and/or
DIHEdral listings should be omitted if the AUTOgenerate ANGL and/or
DIHEdral options are being used (This is now the default). It should
be remembered that autogeneration works in conjunction with the
GENErate command; in PATChes invoked after the initial structure
generation the AUTOGENERATE command must be invoked following the
patch to create the angle and dihedral lists or the angles and
dihedrals must listed explicitly in the patch. As of c31b1 all angles
and dihedrals have been removed from the PRESidues in the topoolgy and
parameter files, EXCEPT in special cases where AUTOGENERATE generate
should not be invoked following patching (eg. certain heme
patches). Note that problems will be encountered if autogeneration is
performed with water molecules present. IMPRoper dihedrals are only
included in special cases and must be listed explicitly. Note that
the central atom should be placed first when defining an improper
dihedral. » parmfile for a rationale.
CMAP (G7), a dihedral crossterm energy correction map that
allows for an explicit 2D energy correction surface to be applied to
any two dihedrals, as specified by the 8 atoms following the CMAP
keyword. The first four atoms represent the first dihedral and the
second four atoms the second dihedral (phi and psi in the present
example). This term is only used in special cases and must be listed
explicitly.
For making hydrogen bond lists the (G8) DONOr and (G9) 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 (G10) 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 (G11) 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 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.
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 H
MASS 2 O 15.99900 O
(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
DOUBLE CA CB
TRIPLE CB CG
(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) CMAP -C N CA C N CA C +N
(G8) DONO H N
(G9) ACCE O C
(G10) 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
(G11) 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
directly followed by (B) the CHARMM version number under which that
particular file was developed. Note that this must be on the line
directly following the title.
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 final column is the atomic type
and is included for compatibility with the MMFF code. 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 listings are always required in order to define the
connectivity of the molecule; BOND can be replaced by DOUBLE, TRIPLE
or AROMATIC allowing for compatibility with MMFF. The ANGLe and/or
DIHEdral listings should be omitted if the AUTOgenerate ANGL and/or
DIHEdral options are being used (This is now the default). It should
be remembered that autogeneration works in conjunction with the
GENErate command; in PATChes invoked after the initial structure
generation the AUTOGENERATE command must be invoked following the
patch to create the angle and dihedral lists or the angles and
dihedrals must listed explicitly in the patch. As of c31b1 all angles
and dihedrals have been removed from the PRESidues in the topoolgy and
parameter files, EXCEPT in special cases where AUTOGENERATE generate
should not be invoked following patching (eg. certain heme
patches). Note that problems will be encountered if autogeneration is
performed with water molecules present. IMPRoper dihedrals are only
included in special cases and must be listed explicitly. Note that
the central atom should be placed first when defining an improper
dihedral. » parmfile for a rationale.
CMAP (G7), a dihedral crossterm energy correction map that
allows for an explicit 2D energy correction surface to be applied to
any two dihedrals, as specified by the 8 atoms following the CMAP
keyword. The first four atoms represent the first dihedral and the
second four atoms the second dihedral (phi and psi in the present
example). This term is only used in special cases and must be listed
explicitly.
For making hydrogen bond lists the (G8) DONOr and (G9) 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 (G10) 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 (G11) 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 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.