Insight II



H       Amino Template File

The amino_template.dat file is used to determine the topology of residues read in from file types that do not supply explicit connectivity or bond order information. For the purposes of this discussion, a residue is a set of atoms that may have their connectivity explicitly determined without looking at their geometry. This may be a peptide, protein, or nucleic acid residue, a complete small molecule, or a monomeric repeat unit in a synthetic polymer. This file also contains information as to what atoms belong to a given charge group, which atom in a charge group is the switching atom, and which atoms are out-of-plane atoms (atoms that are constrained to lie in the in the plane of their substituent atoms). This file is used when reading Brookhaven database files, or Biosym .car, .cor, and .arc files that do not have their normally molecular data files.

Matches are made by first looking for exact name matches with the residue type, and a template entry. If a match is found then the next criterion is the correct number of atoms within the residue. If this test passes, then a final test is made to make sure all of the atom names in the residue and the template match. If all three tests pass, then a match is assumed to have been found. Matches are also made for residues with no hydrogens by subtracting off the number of hydrogens within the template, and comparing the heavy atoms between the residue in the molecule and the template.

The template file is comprised of entries the first line of which is the name of the residue and the number of atoms within it, followed by a line for each atom in the residue which describes fully the unknown information for each atom.

The template file is found in the $BIOSYM/data/insight directory ($INSIGHT_DATA).


File Format Description

Line 1:

Columns 1-4, residue name

123456789_123456789_123456789_123456789_123456789_123456789_123456789_123456789_

ALAnt 11

The first four columns make up the name of the residue, which may be one to four characters in length.

Columns 6-7, number of atoms

123456789_123456789_123456789_123456789_123456789_123456789_123456789_123456789_

ALAn 11

Columns 6-7 specify the number of atoms in the residue, including hydrogens. Separate entries are specified for each of the terminal types of amino acids, and the internal residue.


Line 2:

Columns 1-4, atom name

123456789_123456789_123456789_123456789_123456789_123456789_123456789_123456789_

N pepN 3 1 0 1 1 4 5 1 1 1

The first four columns make up the name of each atom in the residue, which may be one to four characters in length.

Columns 6-9, charge group

123456789_123456789_123456789_123456789_123456789_123456789_123456789_123456789_

N pepN 3 1 0 1 1 4 5 1 1 1

Information in these columns specifies the name of the charge group which contains this atom. This may be one to four characters in length. Each charge group must be contiguous and unique.

Column 11, number of bonded atoms

123456789_123456789_123456789_123456789_123456789_123456789_123456789_123456789_

N pepN 3 1 0 1 1 4 5 1 1 1

This specifies the number of atoms bonded to this atom.

Column 13, connectivity complete flag

123456789_123456789_123456789_123456789_123456789_123456789_123456789_123456789_

N pepN 3 1 0 1 1 4 5 1 1 1

Set to 1, this specifies that the atom's connectivity is specified fully by other atoms within the residue. If it is set to 0, a search is also performed for any atoms that are within range to form bonds. This field is usually set to 1, except for internal amide nitrogens, internal carbonyl carbons, cysteine sulphurs, and nucleic acid linkage points.

Column 15, out-of-plane switch

123456789_123456789_123456789_123456789_123456789_123456789_123456789_123456789_

N pepN 3 1 0 1 1 4 5 1 1 1

Set to 1, this atom is constrained to lie in the plane of its substituent atoms during molecular mechanics simulations. Set to 0, this atom may be non-planar during molecular mechanics simulations. Only atoms with exactly 3 bonds may have this field set to 1.

Column 17, group cutoff switching atom

123456789_123456789_123456789_123456789_123456789_123456789_123456789_123456789_

N pepN 3 1 0 1 1 4 5 1 1 1

Set to 1, this atom is used by Discover to determine whether or not the charge group is to be included in the energy calculation. Discover uses the distance between switching atoms to determine which charge groups are used in energetic calculations. Only one atom per charge group may have this field set to 1.

Columns 19-(19+number bonded atoms, from column 11), bonded atoms

123456789_123456789_123456789_123456789_123456789_123456789_123456789_123456789_

N pepN 3 1 0 1 1 4 5 1 1 1

The atom number of each bonded atom is listed. Atom numbers start at 0 and end at the number of atoms in the residue, less 1. For example, the 1 in column 19 specifies that this atom is bonded to atom number 1 in the residue, which is actually the second atom found in the residue (N is the first, and is atom number 0). The 4 and 5 in columns 21 and 23 specify that this atom is also bonded to the fifth and sixth atoms in the residue. Insight allows up to six bonds per atom.

Columns beyond (19+number bonded atoms), bond order of bonded atoms

123456789_123456789_123456789_123456789_123456789_123456789_123456789_123456789_

N pepN 3 1 0 1 1 4 5 1 1 1

The bond order of each bonded atom is listed in the same order as the bonded atoms. Bond orders are as follows: 0 or 1 is a single bond, 2 is a partial double bond, 3 is a double bond, 4 is a partial triple bond, and 5 is a triple bond.


Example

(extracted from amino_template.dat)


ALA 10
N pepN 2 0 1 1 1 4 1 1
CA pepN 4 1 0 0 2 5 6 0 1 1 1 1
C pepC 2 0 1 1 3 1 3 1
O pepC 1 1 0 0 2 3
HN pepN 1 1 0 0 0 1
HA pepN 1 1 0 0 1 1
CB meB 4 1 0 1 7 8 9 1 1 1 1 1
HB1 meB 1 1 0 0 6 1
HB2 meB 1 1 0 0 6 1
HB3 meB 1 1 0 0 6 1




Last updated December 17, 1998 at 04:29PM PST.
Copyright © 1998, Molecular Simulations Inc. All rights reserved.