Difference between revisions of "Structure-based mutation analysis TSD Journal"
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= Structure preparation = |
= Structure preparation = |
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| − | [https://gist.github.com/ |
+ | [https://gist.github.com/3201833 createPNGs.pml] will perform every necessary task inside Pymol to create a PNG for every frame of the animation. [https://gist.github.com/3201874 createAnimations.sh] will create the final animated gif from these PNGs. |
=Molecular mechanics= |
=Molecular mechanics= |
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Revision as of 22:17, 29 July 2012
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Contents
Structure preparation
createPNGs.pml will perform every necessary task inside Pymol to create a PNG for every frame of the animation. createAnimations.sh will create the final animated gif from these PNGs.
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
