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Labbook 20.01.2015.md

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20.01.2015

Usefull stuff

  • add folders to the .bashrc (located at the home folder)
cd 
vi .bashrc
  • then add the path bash should load each time

Simulation of two heptads

  • 2 hepad long peptide was created using UCSF chimera

    • proline to ϕ = -80 and ψ = 160 (fixes prolines to trans configuration)
    • all other residues ϕ=-179 and ψ=179

  • Verify that the angles are set correctly

g_chi -s CTD.pdb -f CDT.pdb -omega
xmgrace histo-omegaPro.xvg
  • run pdb2gmx, put protein into a dodecahedral box and add water
pdb2gmx -f CTD.pdb -o init.gro -p init.top -ignh -ter -vsite hydrogens -v #CHARMM22STAR
editcomf -f init.gro -o editconf.gro -bt dodecahedron -d 1.5 -center 0 0 0
genbox -cp -editconf.gro -cs spc216 -o genbox.gro -p init.top
  • Run first energy minimization
grompp -f em.md -c genbox.gro -p init.top -o em.tpr
mdrun -v -s em.tpr
  • add ions
genion -s em.tpr -conc 0.15 -o genbox_genion.pdb -neutral -p init.top
  • Energy minimization
grompp -f em.mdp -c genbox_genion.pdb -p init.top -o em.tpr
mdrun -v -s em.tpr -c em.pdb
  • Grompp .tpr file with berendsen.mdp
grompp -f berendsen.mdp -c em.part0001.pdb -p init.top -o md.tpr
  • Connect to the owl3 and enter the password
ssh owl3
  • copy the files already made into a folder energy minimization folder
cd CTD/
mkdir em/
mv * em/
cd ..
mkdir berendsen/
cd em/
cp md.tpr ../berendsen/
  • then run the simulation