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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. These 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 Generation and Manipulation of the Structure.

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 Input-Output Commands 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
(G)   RESI GLY      0.000
(G2)  ATOM N    NH1    -0.35
      ATOM H    H       0.25
      ATOM CA   CH2E    0.10
      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
(H)   PRES CTER      -1.000
(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 CHARMM Emprical Energy Function Parameters) 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 (Generation of Non-bonded Interactions). 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 connectivities, 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. See CHARMM Emprical Energy Function Parameters 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 Input-Output Commands and The Internal Coordinate Manipulation Commands).

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 Generation and Manipulation of the Structure). 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.

For a description of Topology, Parameter and Stream Files available in CHARMM see PARMFILE.doc.