Up: Specification of Potentials
This type specifies the Structure-Based G
-like models (SBMs). A separate potential file called SBM.INP needs to be provided in the folder where OPTIM is run. SBM.INP describes parameters for bonds, angles, dihedrals and pairs of residues in contact. For generating SBM.INP, see SMOG2. The SB routines in OPTIM apply switching functions to non-bonded terms. The switching range (r0 to rc) is defined on the third line of SBM.INP. The switching function is defined as a fourth-order polynomial, which ensures the force continuously reaches zero at rc. Also see Go-kit for PYTHON tools to generate SBM.INP and GROMACS compatible topology files. Subroutines used:SBM.