Difference between revisions of "Structure-based mutation analysis TSD Journal"
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[https://gist.github.com/2972452 callMinimise.sh] handles all runs, including the five additional iterations per structure |
[https://gist.github.com/2972452 callMinimise.sh] handles all runs, including the five additional iterations per structure |
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==Gromacs== |
==Gromacs== |
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− | The mutation modelling was done with |
+ | The mutation modelling was done with |
− | run_muts.sh |
+ | [https://gist.github.com/2995477 run_muts.sh] . |
− | The time/step calculations were computed with |
+ | The time/step calculations were computed with |
− | time.pl ## This was adapted from [[Task7_Hemochromatosis_Protocol#Gromacs]] |
+ | [https://gist.github.com/2995485 time.pl] ## This was adapted from [[Task7_Hemochromatosis_Protocol#Gromacs]] . |
+ | |||
+ | The Gromacs energies were extracted with [https://gist.github.com/3023195m allGromacsEnergies.sh] . |
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Mdp file explanation: |
Mdp file explanation: |
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# Neighbour searching - Use no periodic boundary conditions, ignore the box. |
# Neighbour searching - Use no periodic boundary conditions, ignore the box. |
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pbc = no |
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.
Contents
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