Difference between revisions of "Structure-based mutation analysis TSD Journal"

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Back to [[Structure-based_mutation_analysis_TSD|results]].
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= Structure preparation =
  
= Structure preparation =
 
[https://gist.github.com/2966700 prepareFiles.pml] applies all necessary changes to the entry 2gjx from the PDB.
  
[https://gist.github.com/2966700 prepareFiles.pml] applies all necessary changes to the entry 2gjx from the PDB.
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==FoldX==
  
==FoldX==
 
[https://gist.github.com/2969611 callFoldx.sh] contains the code to run FoldX and also links to the configuration files.
  
[https://gist.github.com/2969611 callFoldx.sh] contains the code to run FoldX and also links to the configuration files.
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==Minimise==
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[https://gist.github.com/2972452 callMinimise.sh] handles all runs, including the five additional iterations per structure
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==Gromacs==
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The mutation modelling was done with
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[https://gist.github.com/2995477 run_muts.sh] .
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The time/step calculations were computed with
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[https://gist.github.com/2995485 time.pl] ## This was adapted from [[Task7_Hemochromatosis_Protocol#Gromacs]] .
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The Gromacs energies were extracted with [https://gist.github.com/3023195m allGromacsEnergies.sh] .
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Mdp file explanation:
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title = PBSA minimization in vacuum
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cpp = /usr/bin/cpp
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# Preprocessing
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# -DFLEXIBLE: include flexible water in stead of rigid water into topology
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# -DPOSRES: includes posre.itp into topology, used for position restraints.
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define = -DFLEXIBLE -DPOSRES
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# Implicit solvent - simulation with implicit solvent using the Generalized Born formalism
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implicit_solvent = GBSA
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# Run control - steepest descent algorithm for energy minimization
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integrator = steep
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# Run control - tolerance
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emtol = 1.0
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# Run control - maximum number of steps to integrate or minimize
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nsteps = 500
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# Output - frequency of energies to energy file
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nstenergy = 1
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# Tables - group(s) to write to energy file
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energygrps = System
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# Neighbour searching - makes grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list every nstlist steps
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ns_type = grid
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# Electrostatics - twin range cut-off's with neighborlist cut-off rlist and Coulomb cut-off rcoulomb
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coulombtype = cut-off
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rcoulomb = 1.0
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# VDW - distance for the LJ or Buckingham cut-off
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rvdw = 1.0
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# Bonds - no constraints except for those defined explicitly in the topology
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constraints = none
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# Neighbour searching - Use no periodic boundary conditions, ignore the box.
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pbc = no
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===Plots===
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The energy plots were done with [https://gist.github.com/3023187 gromacsEnergies.R]

Latest revision as of 22:18, 29 July 2012

Back to results.

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

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