D. The Geometric Structure Definition File

This file provides the definitions of the common amino acids in terms of their atomic composition, intra-residue bonds and structural geometry. The data is used in:

the Protein Special bonding algorithm, which finds the bonds on the basis of atom name irrespective of geometry;

the Protein Editor to generate geometrically ideal (though not necessarily energetically good) structures for mutation and insertion and also for editing terminal groups;

regularization used in several places in Protein Design and the X- ray module.

Split and Clean to provide the definition of correct protein structure

Note that whether an amino acid is recognized as such and displayed in the Sequence Viewer depends on the data in $HYD_LIB/protein_param.dat after the keyword AMINO. The protein_structure.gsd supersedes the data in the template files $HYD_LIB/tmplatnoh/*.pdb, $HYD_LIB/tmplatpol/*.pdb and $HYD_LIB/tmplatall/*.pdb which was used in the Protein Editor utility for mutation and insertion and the list of bonded atoms in $HYD_LIB/protein_torsion.dat used in the Protein Special bonding algorithm.

The default versions of this file are $HYD_LIB/protein_structure.gsd and its binary version $HYD_LIB/protein_structure.bgsd. The binary version of the file is normally read by QUANTA as this speeds up the access considerably.

If you need to edit the geometric structure file, copy the ascii file to your own directory, edit it and then run QUANTA and type in the command line TMPL. You will be asked for the name of the ASCII file, which is converted to binary. QUANTA then reads your local copy of protein_structure.bgsd (in either the current working directory or your data directory) in preference to the version in $HYD_LIB.

The file format

The file uses four-letter keywords to identify data. The data is read free format, so exact formatting is not necessary but the spaces between are essential.

NAME code full_name

code: a short name of four or fewer characters

full_name: name of maximum 40 characters

TYPE type

type: the functional type of the group.

The recognized types are: PROTEIN_N_TERMINAL, PROTEIN_C_ TERMINAL, PROTEIN_MAIN, PROTEIN_SIDE

GROUp n_atoms

n_atoms: number of atoms in the group as defined after the following n_atoms lines.

name x y z type_allH charge_allH type_polarH charge_polarH type_noH charge_noH

name: maximum four character atom name

x,y,z: coordinates for this atom in a group of ideal geometry.

type_allH, charge_allH: the atom type and charge for an all atom representation of the group

type_polarH, charge_polarH: the atom type and charge for a polar hydrogen only representation of the group

type_noH, charge_noH: the atom type and charge for a no hydrogen representation of the group

Here the atom types use the QUANTA number scheme which corresponds to CHARMm atom types. The atom types are listed in the file $HYD_LIB/param.par Where a hydrogen atom is excluded from a representation it is given an atom type of zero.

TEMPlate

is followed by three lines of:

name x y z

name atom name of maximum four characters x y z coordinates

The template is the three neighboring atoms to a group which are used, for example in mutating a protein side chain, as a guide for positioning the group.

BOND name_1 name_2 .... name_10

name_1 name_2...: a list of maximum five pairs of atom names which indicate the bonded atoms

IMPRoper representation name_1 name_2 name_3 name_4

defines any improper dihedrals

representation: the minimal hydrogen representation for which the improper is valid. For example, an improper involving a polar hydrogen would not be valid in a no-hydrogen representation so the appropriate representation term is "POLAR_H". The recognized terms are: NO_H, POLAR_H, ALL_H.

name_1 ... name_4: names of four atom which should be constrained by an improper dihedral.

DIHEdral representation name_1 name_2 name_3 name_4 angle

Identify dihedral torsions in the group representation: minimal hydrogen representation for which dihedral is appropriate - see explanation after the IMPRoper keyword.

name_1 ... name_4: names of four atom which define the dihedral

angle: the optimal value of the dihedral

RETYpe old_name new_name type_allH charge_allH type_polarH charge_polarH type_noH charge_noH

Where the addition of a group to a residue causes a change in the atom name, type or charge of another atom in the residue this keyword is used to define the new name, type and charge.

old_name: old atom name

new_name: new atom name

type_allH, charge_allH: the new type and charge for the atom assuming an all atom representation

type_polarH, charge_polarH: the new type and charge for the atom assuming an polar hydrogen representation

type_noH, charge_noH: the new type and charge for the atom assuming a no-hydrogen representation

ALTName name alt_name:

where atoms in a residue have alternative names in common use name is the atom name used here and alt_name is the alternative name.