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The AMBER 94 parameter set1 is available as AMBER94PARM. This parameter file must be used with the AMBER 94 topology file, see AMBER94RTF.

Several atoms in the AMBER94 potential have zero van der Waals radii. This causes problems for CONGEN because of the possibility that such atoms may get close enough to another atom for electrostatic fusion to occur. Therefore, such atoms have been given a small van der Waals radius and a small van der Waals repulsive interaction. Please see the file for the exact value.

This potential file has some features which you should be aware of. First, the amide torsion terms (as found in the aspargine and glutamine sidechains) are designed so that the minimum energy is non-zero, and the shape is correct only when both hydrogens are considered. Second, there is no explicit hydrogen bond energy. Such interactions are accounted for by the electrostatic energy. Third, zero energy improper torsion terms have been added for chiral centers so that the analysis tables, see Internal Coordinate Properties, will show the chirality and allow the user to check it.


[1] Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, Ian R. Gould, Kenneth M. Merz, Jr., David M. Furguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell and Peter A. Kollman, “A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules”, J. Am. Chem. Soc. 117, 5179-5197 (1995)