Structure-based mutation analysis TSD Journal

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Structure preparation

prepareFiles.pml applies all necessary changes to the entry 2gjx from the PDB.

Molecular mechanics

SCWRL

allmuts_*.sh creates the necessary files for SCWRL and also runs it on them.

FoldX

callFoldx.sh contains the code to run FoldX and also links to the configuration files.

Minimise

callMinimise.sh handles all runs, including the five additional iterations per structure

Gromacs

The mutation modelling was done with run_muts.sh .

The time/step calculations were computed with time.pl ## This was adapted from Task7_Hemochromatosis_Protocol#Gromacs .

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

Plots

The energy plots were done with gromacsEnergies.R