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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

Xplor-NIH 2024-09-13