Structure-based mutation analysis TSD Journal
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prepareFiles.pml applies all necessary changes to the entry 2gjx from the PDB.
allmuts_*.sh creates the necessary files for SCWRL and also runs it on them.
callFoldx.sh contains the code to run FoldX and also links to the configuration files.
callMinimise.sh handles all runs, including the five additional iterations per structure
The mutation modelling was done with run_muts.sh .
The Gromacs energies were extracted with allGromacsEnergies.sh .
Mdp file explanation:
title = PBSA minimization in vacuum cpp = /usr/bin/cpp # Preprocessing # -DFLEXIBLE: include flexible water in stead of rigid water into topology # -DPOSRES: includes posre.itp into topology, used for position restraints. define = -DFLEXIBLE -DPOSRES # Implicit solvent - simulation with implicit solvent using the Generalized Born formalism implicit_solvent = GBSA # Run control - steepest descent algorithm for energy minimization integrator = steep # Run control - tolerance emtol = 1.0 # Run control - maximum number of steps to integrate or minimize nsteps = 500 # Output - frequency of energies to energy file nstenergy = 1 # Tables - group(s) to write to energy file energygrps = System # Neighbour searching - makes grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list every nstlist steps ns_type = grid # Electrostatics - twin range cut-off's with neighborlist cut-off rlist and Coulomb cut-off rcoulomb coulombtype = cut-off rcoulomb = 1.0 # VDW - distance for the LJ or Buckingham cut-off rvdw = 1.0 # Bonds - no constraints except for those defined explicitly in the topology constraints = none # Neighbour searching - Use no periodic boundary conditions, ignore the box. pbc = no
The energy plots were done with gromacsEnergies.R