Skip to main content
U.S. flag

An official website of the United States government

Here’s how you know

Official government website icon

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

icon-https

Secure .gov websites use HTTPS
A lock ( Lock Locked padlock icon )or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

NIH: National Institute of Diabetes and Digestive and Kidney Diseases NIH: National Institute of Diabetes and Digestive and Kidney Diseases

  next up previous contents index  Xplor-NIH home Documentation

Next: Syntax Up: Topology, Parameters and Molecular Previous: Files “parallhdg.dna" and “topallhdg.dna"


Generating the Molecular Structure

The segment statement generates the molecular structure by interpreting the coordinate file to obtain the residue sequence or by explicitly specifying the residue sequence. The residues have to be defined in the topology statement (Section 3.1.1). A segment is defined as a protein with one continuous polypeptide chain, a continuous polypeptide chain itself, a substrate, a cofactor, a ligand, a set of water molecules, or a single nucleic acid strand. For a combination of proteins, water, substrates, ligands, and/or nucleic acids, the user should first split the original coordinate file into several files containing the segments, generate each segment separately, and, if necessary, apply appropriate patches to establish covalent links between segments or within segments, such as disulfide bridges.


Subsections
  • Syntax
  • Requirements
  • Example: A Polypeptide Chain
  • Example: A Polypeptide Chain with an Unknown Section
  • Example: Water Molecules
  • Example: Solvation of a Solute


Xplor-NIH 2025-03-21
  • Privacy Policy
  • Freedom of Information Act
  • Accessibility
  • Disclaimers
  • Copyright
  • Vulnerability Disclosure Policy
  • U.S. Department of Health and Human Services
  • National Institutes of Health