SSRestraints Plugin, Version 1.1

The ssrestraints plugin generates an extraBonds file to apply harmonic restraints to secondary structure elements using NAMD. The extraBonds feature of NAMD allows a user to define additional bonds, angles, dihedrals or impropers.

Restraining protein secondary structure

In order to restrain protein secondary structure, ssrestraints creates additional dihedrals corresponding to phi and psi angles. The equilibrium value for the dihedral angles are set to the values in the given structure. By default, every protein residue that is part of a helix or a beta sheet is restrained, but an arbitrary selection can be restrained instead. Protein backbone H-bonds can also be restrained with the option -hbonds. If the option -hbonds is used, backbone H-bonds found in helices or beta sheets are restrained by default, but an arbitrary selection for H-bond donors and acceptors can be given instead.

Restraining nucleic acid secondary structure

To restrain RNA secondary structure, ssrestraints uses the RNAView plugin to identify and classify base pairs. Harmonic restraints are defined based on the base pairing information as described in Publications Database Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Leonardo G. Trabuco, Elizabeth Villa, Kakoli Mitra, Joachim Frank, and Klaus Schulten. Structure, 16:673-683, 2008.

Usage information

Usage: ssrestraints -psf <input psf> -pdb <input pdb> -o <output file> ?options?
Options:
  -sel <selection text> (default: helix or extended_beta or nucleic)
  -k_prot <force constant for protein dihedrals> (default: 200)
  -k_na_bond <force constant for the nucleic acid bonds> (default: 200)
  -k_na_dih <foce constant for the nucleic acid dihedrals> (default: 200)
  -ideal -- reference to ideal alpha helices, 3-10 helices, and beta strands
  -labels -- add labels for visualization of restraints
  -hbonds -- restrain H-bonds
  -hbdonorsel <H-bond donor selection text> (default: name N and backbone and (helix or extended_beta))
  -hbaccsel <H-bond acceptor selection text> (default: name O and backbone and (helix or extended_beta))
  -hbbondk <force constant for H-bonds> (default: 20.0)
  -hbanglek <force constant for H-bonds> (default: 20.0)
  -hbdcut <H-bond distance cut-off in Angstroms> (default: 3.5)
  -hbacut <H-bond angle cut-off in degrees> (default: 35.0)
  -na <restraints for nucleic acid> (default: 3)
      0: dihedrals of all residues
      1: dihedrals of base-paired residues
      2: two bonds between base paired residues
      3: both options 1 and 2

Authors

Leonardo Trabuco and Elizabeth Villa.