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Symmetric Linkage

Symmetric linkages are referred to covalent bonds, bond angles and dihedral angles involving atoms in different but symmetrically related subunits. The symmetric_linkage statement is used to create a data base describing the symmetric linkages between symmetric related subunits for potential energy calculations. After the symmetric linkages are defined, the non-bonded interactions between atoms linked by the symmetric linkages become invalid. These non-bonded interactions must be removed from the table of non-bonded intersubunit interactions. Exclusion of these invalid non-bonded interactions should be defined in the data base using either AUTOexclude or EXCLude statements.

The symmetric_linkage data base is not stored in the structure file (PSF file). Therefore, the symmetric_linkage-statements have to be entered every time when the information is required for the non-bonded energy calculations.

Subsections

Xplor-NIH 2025-11-07