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Next: CHARMM “top_all22*" and “par_all22*" Up: Topology, Parameters and Molecular Previous: Example: Reducing Parameters Learned
Topology and Parameter Files
This section describes the most important parameter and
topology files that are distributed with X-PLOR. A pair
of parameter and topology files represents a force field or empirical
energy function. Force fields
are supplied for proteins, nucleic acids, carbohydrates, and
lipids, as well as a number of other biological molecules.
All parameter files represent polar hydrogens (i.e., hydrogens
that can form hydrogen bonds) explicitly, whereas aliphatic
hydrogens are either explicitly included or implicitly modeled
by appropriate modification of the heavy-atom van der Waals
parameters. A number of specialized force fields are
available for X-ray crystallographic or NMR-spectroscopic
structure determination. All parameter and topology files
can be found in the “toppar" directory.
Subsections
- CHARMM “top_all22*" and “par_all22*" All Hydrogen Force Field
- CHARMM “toph19.pro" and “param19.pro" Files for Proteins (Explicit Polar Hydrogens)
- CHARMM “toph11.dna" and “param11.dna" Files for Nucleic Acids (Explicit Polar Hydrogens)
- Files “topnah1e.dna" and “parnah1e.dna" for Nucleic Acids (Explicit All Hydrogens)
- AMBER/OPLS “tophopls.pro", “parhopls.pro" Files (Explicit Polar Hydrogens)
- Files “toph19.sol" and “param19.sol" for Water (TIP3p Model)
- Files “toph3.cho" and “param3.cho" for Carbohydrates
- Files “toph19.chromo" and “param19.chromo" for Chromophores
- Files “parhcsdx.pro" and “tophcsdx.pro" for Crystallographic Refinement (Polar Hydrogens)
- Files “parallhdg.pro" and “topallhdg.pro" for
NMR Structure Determination of Proteins (All Hydrogens)
- Files “parallhdg.dna" and “topallhdg.dna" for NMR Structure Determination of Nucleic Acids (All Hydrogens)
Xplor-NIH 2024-09-13