This section describes the parameter and topology files that are distributed with CNS. Topology and parameter files together represents a particular force field or empirical energy function. Files are supplied for proteins, nucleic acids, carbohydrates, water and ions. Most topology and parameter files contain 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. For most crystallographic applications these hydrogen atoms are not used. The force fields are specialized for X-ray crystallographic or NMR-spectroscopic structure determination. All parameter and topology files can be found in the "libraries/toppar" directory.
This describes the topology for protein building blocks (amino acids) including polar hydrogens. It also contains patches for peptide linkages, N- and C-terminal ending groups, the disulphide bond and histine protonation states.
protein_nohydrogen.topThis describes the topology for protein building blocks (amino acids) without any hydrogen atoms. It also contains patches for peptide linkages, N- and C-terminal ending groups, the disulphide bond and histine protonation states. This topology file should be used when the structure is very large and the addition of hydrogens (even only temporarily during molecular topology generation) creates problems.
protein.linkThis describes the linkage between protein building blocks (amino acids). It also contains the information about which N- and C-terminal ending groups are to be applied. This is not specific to crystallography or NMR.
protein_rep.paramThis parameter file describes the parameters for proteins and should be used in conjunction with other parameter files which use a repulsive force field (protein_rep.param and dna-rna_rep.param). This is the suggested parameter set for crystallographic refinement.
protein.paramThis parameter file describes the parameters for proteins and should be used in conjunction with other parameter files which do not use a repulsive force field (protein.param and dna-rna.param).
protein_break.topThis describes patches for the deletion of peptide linkages.
This describes the topology for nucleic acid building blocks (nucleotides) including polar hydrogens. It also contains patches for nucleotide linkages, and 3' and 5'-terminal ending groups.
dna-rna.linkThis describes the linkage between nucleic acid building blocks (nucleotides). It also contains the information about which 3' and 5'-terminal ending groups are to be applied. Neither 3' or 5' ends of the nucleic acid have a phosphate attached. This is not specific to crystallography or NMR.
dna-rna-pho.linkThis describes the linkage between nucleic acid building blocks (nucleotides). It also contains the information about which 3' and 5'-terminal ending groups are to be applied. A phosphate group is applied to the 5' end of the nucleic acid. This is not specific to crystallography or NMR.
dna-rna_rep.paramThis parameter file describes the parameters for nucleic acids and should be used in conjunction with other parameter files which use a repulsive force field (protein_rep.param and dna-rna_rep.param). This is the suggested parameter set for crystallographic refinement.
dna-rna.paramThis parameter file describes the parameters for nucleic acids and should be used in conjunction with other parameter files which do not use a repulsive force field (protein.param and dna-rna.param).
This describes the topology for carbohydrate building blocks (sugars) including polar hydrogens. It also contains patches for linkages between different sugars.
carbohydrate.paramThis parameter file describes the parameters for carbohydrates and can be used in conjunction with any other parameter files. The parameters may need modification to be consitant with other parameter sets (in paarticular the force constants for impropers and dihedrals are low compared to the other crystallographic parameter sets).
This describes the topology for many elements and ionic species of elements. Topology definitions also exist for ions such as sulphate, phosphate and tungstate.
ion.paramThis parameter file describes the parameters for ions and can be used in conjunction with any other parameter files.
This describes the water molecule topology using a variety of residue and atom naming.
water_protin.topThis describes the water molecule topology using the CCP4 PROTIN residue naming convention.
water_rep.paramThis parameter file can be used in conjunction with other parameter files which use a repulsive force field (protein_rep.param and dna-rna_rep.param). This is the suggested file for crystallographic refinement.
water.paramThis parameter file can be used in conjunction with other parameter files which do not use a repulsive force field (protein.param and dna-rna.param). The file also contains special adjustments for solvent-solute interactions.
This describes the topology for protein building blocks (amino acids) including all hydrogens. It also contains patches for peptide linkages, N- and C-terminal ending groups, the disulphide bond, histine protonation states and L- to D-amino acid conversion.
protein-allhdg.paramThis parameter file describes the parameters for proteins and should be used in conjunction with other parameter files which use an all atom force field. This is the suggested parameter set for NMR structure calculation.
protein.linkThis describes the linkage between protein building blocks (amino acids). It also contains the information about which N- and C-terminal ending groups are to be applied. This is not specific to crystallography or NMR.
This describes the topology for nucleic acid building blocks (nucleotides) including all hydrogens. It also contains patches for nucleotide linkages, and 3' and 5'-terminal ending groups.
dna-rna-allatom.paramThis parameter file describes the parameters for nucleic acids and should be used in conjunction with other parameter files which use an all atom force field. This is the suggested parameter set for NMR structure calculation.
dna-rna.linkThis describes the linkage between nucleic acid building blocks (nucleotides). It also contains the information about which 3' and 5'-terminal ending groups are to be applied. Neither 3' or 5' ends of the nucleic acid have a phosphate attached. This is not specific to crystallography or NMR.
dna-rna-pho.linkThis describes the linkage between nucleic acid building blocks (nucleotides). It also contains the information about which 3' and 5'-terminal ending groups are to be applied. A phosphate group is applied to the 5' end of the nucleic acid. This is not specific to crystallography or NMR.
The sigma values in the parameter file protein-allhdg.param are different from those used in the other all-hydrogen force fields. The changes were made to make the van der Waals radii more consistent with those used by other NMR refinement programs. The sigma values have been set such that the van der Waals radii will be exactly like those used by the DISGEO program (Havel and Wuthrich 1984) when REPEl is set to 0.8. In addition, van der Waals radii of potential hydrogen bond donor-acceptor pairs have been reduced by appropriate NBFIx statements. The actual van der Waals radii used for different values of REPEl are given in the table below (in A).
| type | repel=1.0 | repel=0.9 | repel=0.8 | repel=0.75 |
| H | 1.250 | 1.125 | 1.0 | 0.938 |
| C | 1.875 | 1.688 | 1.5 | 1.406 |
| N | 1.688 | 1.519 | 1.350 | 1.266 |
| O | 1.558 | 1.402 | 1.246 | 1.168 |
| S | 2.102 | 1.892 | 1.682 | 1.577 |
It should be noted that the van der Waals radii in protein-allhdg.param are not appropriate for use with the standard Lennard-Jones potential.
Convention for Hydrogen NamesThe hydrogen names follow the scheme that is adopted by the CHARMM all-hydrogen force fields (Brooks et al. 1983). If a different scheme is required, the user can either rename the hydrogens in the topology file or change the molecular structure after it has been created.