Calculate multiple dihedral angles of specified/given types.
multidihedral [<name>] <dihedral types> [resrange <range/mask>] [out <filename>] [range360] [dihtype <name>:<a0>:<a1>:<a2>:<a3>[:<offset>] ...] Offset -2=<at0><at1> in previous res, -1=<at0> in previous res, 0=All <atX> in single res, 1=<at3> in next res, 2=<at2><at3> in next res. <dihedral types> = alpha beta gamma delta epsilon zeta phi psi chip omega chi2 chi3 chi4 chi5 nu0 nu1 nu2 nu3 nu4 hip c2p chin
[<name>] Output data set name.
<dihedral types> Dihedral types to look for. Note that chip is ’protein chi’, chin is ’nucleic chi’.
[resrange <range/mask>] Residue range to look for dihedrals in. Default is all solute residues. If a mask expression is given, use residues selected by the mask expression; if any part of a residue is selcted it will be used.
[out <filename>] Output file name.
[range360] Wrap torsion values from 0.0 to 360.0 (default is -180.0 to 180.0).
[dihtype <name>:<a0>:<a1>:<a2>:<a3>[:<offset>] Search for a custom dihedral type called <name> using atom names <a0>, <a1>, <a2>, and <a3>.
Offset: -2=<a0><a1> in previous res, -1=<a0> in previous res, 0=All <aX> in single res, 1=<a3> in next res, 2=<a2><a3> in next res.
<name> [<dihedral type>]: <#> Aspect corresponds to the dihedral type name (e.g. [phi], [psi], etc). The index is the residue number
Note data sets are not generated until run is called.
Calculate specified dihedral angle types for residues in given range. By default, dihedral angles are identified based on standard Amber atom names. The resulting data sets will have aspect equal to [<dihedral type>] and index equal to residue #. To differentiate the chi angle, chip is used for proteins and chin for nucleic acids. For example, to calculate all phi/psi dihedrals for residues 6 to 9:
multidihedral MyTorsions phi psi resrange 6-9 out PhiPsi_6-9.dat
Dihedrals other than those defined in <dihedral types> can be searched for using dihtype. For example to create a custom dihedral type called chi1 using atoms N, CA, CB, and CG (all in the same residue), then search for and calculate the dihedral in all residues:
multidihedral dihtype chi1:N:CA:CB:CG out custom.dat