PDB2GROUP(1)

NAME

pdb2group - generate Midas group file from Protein Data Bank (PDB) file

SYNOPSIS

pdb2group -a anchor_atom -3 n3_atom -2 n2_atom [ -d
group_description ] [ PDB_file ]

DESCRIPTION

Pdb2group takes a PDB file with explicit CONECT records (even for standard residues such as amino acids) and generates a ``group'' file suitable for use with midas(1). The group file is used by MIDAS commands such as swapaa, swapna, and addgrp, and defines the connectivity and relative position of a group of atoms. The generated group file is written to standard output.

FILE FORMAT

     A group file consists of a series of text lines, and can be
     divided into four parts.  The first part is the title and is
     a single-line description of the group, e.g., 4-OH-phenyl.
     The second part is the list of atoms in the group and is a
     series of lines of the form
          new atom_name x y z

     The atom names should be in uppercase letters and need not
     be unique.  The Cartesian coordinates specified by these
     lines are generally ignored by most programs, and may be set
     to (0, 0, 0) if they are not conveniently available.  The
     third part of file group file is a separator and is a single
     line:
          read internal coordinates for new group

     The fourth and final part of the group file is the
     connectivity and relative position description and is a
     series of lines of the form
          mode atom1 atom2 atom3 atom4 bond_length bond_angle
          dihedral_angle
The mode field of the line is a single character, either `+' or `=,' and is generally ignored. Each of the four atom fields may be either a number, or n3, n2, or n1. If it is a number, it refers to an atom in the group. The atoms listed in the group are numbered sequentially, with the first atom being 0. If the atom field is one of the special strings, it refers to an atom in the molecule to which the group will be attached. Atom 0 is always attached to atom n3. The bond length is the distance between atom1 and atom2. The bond angle is the angle formed by atom1, atom2, and atom3, with atom2 as the vertex. The dihedral angle is the angle formed by all four atoms, with atom2 and atom3 as the internal vertices.

An example of a group file, for 4-hydroxy-phenol, follows:
4-OH-phenyl new C 0.000 0.000 0.000 new C 0.000 0.000 0.000 new C 0.000 0.000 0.000 new C 0.000 0.000 0.000 new O 0.000 0.000 0.000 new C 0.000 0.000 0.000 new C 0.000 0.000 0.000 read internal coordinates for new group + 1 0 n3 n2 1.4 120.0 60.0 + 2 1 0 n3 1.4 120.0 180.0 + 3 2 1 0 1.4 120.0 0.0 = 4 3 2 1 1.37 120.0 180.0 + 5 3 2 1 1.4 120.0 0.0 + 6 5 3 2 1.4 120.0 0.0 + 6 0 1 2 1.4 120.0 0.0

Group file format is also described in detail in ``Chemical Group Description Files'' in part 3 of the MidasPlus manual.

COMMAND ARGUMENTS

The required command-line arguments to pdb2group are the names of anchor_atom, n3_atom, and n2_atom. The anchor_atom is the first atom to be listed in the computed group file. N3_atom and n2_atom refer to atoms in PDB_file and are used to compute bond and dihedral angles between the group and the rest of the molecule; they do not appear in the group file. Atoms in the PDB file which are connected to anchor_atom only through n3_atom will not appear in the group file. The PDB file must contain only one residue.

The title of the group file is the group_description, if given, or the PDB file name otherwise. If the PDB file is read from standard input, the title is ``-.''

EXAMPLE

Although lysine is provided as a standard group, for purposes of illustration the derivation of a group file describing a lysine side-chain is shown here.

Creating the PDB input file
Creating the PDB input file by hand is a tedious procedure, but may be necessary if you have no PDB file containing the desired group, and no model-building tools are available. If so, refer to ``Protein Data Bank Format'' in part 3 of the MidasPlus User's Manual for the exact format description. You would need to create a file containing a single residue containing the group of interest, with explicit CONECT records for all atoms in the file.

     A much more pleasant alternative, if you have a PDB file on
     hand with the group in it, or can make a basic PDB file
     containing the group that MIDAS can display, is to use MIDAS
     to generate the final PDB input file.  The procedure would
     be to open the starting PDB file in MIDAS, limit the display
     to the residue of interest, and then run the command:
          pdbrun conect nouser cat > final_PDB_input_file

     To continue the example of generating a lysine side-chain
     group description file, if the standard PDB entry 1gcn were
     open in MIDAS as model 0, then the following commands would
     be used:
          show #0:12                 display only lysine residue
          pdbrun conect nouser cat > lyssagvreouPpD.Binfile with CONECT records into ``lysgroup.in''
Running pdb2group
Referring to the SYNOPSIS section above, the anchor_atom specified on the command line should be the first added atom of the new group when the group is added to an existing structure. N3_atom and n2_atom are atoms that are not in the new group, but that the new group connects to. N3_atom connects directly to the anchor_atom, and n2_atom connects to n3_atom.

     So in the lysine group example, the appropriate pdb2group
     command would be:
          pdb2group -a CB -3 CA -2 C -d Lysine lysgroup.in >
          lysgroup.out

SEE ALSO

MidasPlus User's Manual

AUTHORS

Conrad Huang, UCSF Computer Graphics Laboratory