A.6.5 AMBER94RTF

This file contains the AMBER 94 all atom topology file. There is no united atom topology file available for this parameter set. Whenever this topology file is used, the automatic generation options in the GENERATE command, see Generate Command, will be turned on by default. This file must be used with the AMBER 94 parameter file, see AMBER94PARM.

This file contains the standard amino acids, several charge variants for polar amino acids, amino and carboxy terminal amino acids, and DNA and RNA nucleotides with no terminations, terminations on each end, and single complete nucleotides. In addition, D amino acids are also present. These are generated by inverting all the construction rules for the L amino acids, so that all the chiralities are changed, including those involving just nomenclature.

Atom names in this topology file are somewhat different from those used in the previous CHARMM and CONGEN topology files. It is intended to provide closer adherence to the IUPAC naming, see Syntactic Glossary, so that it will be easier to read Brookhaven Protein Data Bank files.

A new mechanism for patching the ends of a protein or nucleic acid is used with this topology file. The topology file stores different versions of each residue for each end as well as for interior positions. When a segment is generated, see Generate Command, the appropriate end residue will be used, but the final name of the residue will be reset to the original name. Thus, the terminal residues will have the usual name, and no terminal residues, like NTER or CTER, will be used.

The URL, http://www.amber.ucsf.edu/amber/amber.html, was the source for data in this file.