Insight II

E       Hydrogen Bonds

Following are the contents of the Insight II template file named hbond_file.dat. This file contains the atoms considered in hydrogen bonding. The first line defines the default minimum angle. For example:

Angle:      120.0.

 The five columns are:

1. Name of the monomer/residue in which the following donor atom is found (an asterisk denotes all monomers/residues).

2. Name of the donor atom (a letter followed by an asterisk denotes any match on the letters following the first).

3. Name of the monomer/residue in which the following acceptor atom is found.

4. Name of the acceptor atom.

5. Maximum distance the two atoms can be apart to be considered hydrogen bonded (in angstroms).

Note that heavy atoms with no hydrogens which could be involved in hydrogen bonding are included by specifying the minimum distance for the two heavy atoms.

Monomer/ Donor Monomer/ Acceptor Hydrogen
Residue Name Residue Name Bonding
-Name Name Distance

* H* * N* 2.5

* H* * O* 2.5

* H* * S* 2.5

* N* * O* 3.0

* N* * S* 3.7

* O* * O* 3.0

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