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
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.