ssrestraints¶
Secondary-structure restraints generated by the VMD ssrestraints plugin and applied via NAMD’s extraBonds facility
Single-valued attributes:
sel: VMD atomselect text passed to ssrestraints -sel; restricts which residues are restrained (default: helix or extended_beta or nucleic)
k_prot: Force constant for protein phi/psi dihedral restraints (kcal/mol/rad^2) (default: 200)
k_na_dih: Force constant for nucleic-acid backbone dihedral restraints (kcal/mol/rad^2) (default: 200)
k_na_bond: Force constant for nucleic-acid base-pair bond restraints (kcal/mol/A^2) (default: 200)
na: Nucleic-acid restraint mode: 0=all-residue dihedrals; 1=base-paired-residue dihedrals; 2=base-pair bonds; 3=both 1 and 2 (default: 3)
ideal: Use ideal phi/psi for alpha/3-10 helix and beta strand instead of measured values (default: False)
hbonds: Add backbone H-bond bond+angle restraints (default: False)
hbdonorsel: VMD atomselect text identifying H-bond donor heavy atoms (default: name N and backbone and (helix or extended_beta))
hbaccsel: VMD atomselect text identifying H-bond acceptor heavy atoms (default: name O and backbone and (helix or extended_beta))
hbbondk: Force constant for the H-bond bond term (kcal/mol/A^2) (default: 20.0)
hbanglek: Force constant for the H-bond angle term (kcal/mol/rad^2) (default: 20.0)
hbdcut: H-bond donor-acceptor distance cutoff used during detection (Å) (default: 3.5)
hbacut: H-bond donor-H-acceptor angle cutoff used during detection (degrees) (default: 35.0)