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李毅笔记.md

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source /usr/local/gromacs/bin/GMXRC

analysis trajectory

basic file handler

select protein with periodic boundary conditions fixed

echo Protein-H | gmx_mpi trjconv -f md.xtc -s md.tpr -o pro.xtc -pbc mol -ur compact

echo C-alpha | gmx_mpi trjconv -f md.xtc -s md.tpr -o ca.xtc -pbc mol -ur compact

echo Backbone | gmx_mpi trjconv -f md.xtc -s md.tpr -o bb.xtc -pbc mol -ur compact

echo Backbone | gmx_mpi trjconv -f md.xtc -s md.tpr -n /home/gerry/gp120/stru/3j70.ndx -o pro.xtc -pbc mol -ur compact

look at your trajectory first using VMD

convert xtc to using Mdtraj command line

mdconvert pro.xtc -o pro.dcd
mdconvert ca.xtc -o ca.dcd

energies

echo Potential | gmx_mpi energy -f md.edr -o energy.xvg

RMSD

echo Backbone Backbone | gmx_mpi rms -f md.xtc -s md.tpr -o rmsd.xvg -tu ns
echo Backbone Backbone | gmx_mpi rms -f md.xtc -s gp120.pdb -o rmsd_str.xvg -tu ns
echo Backbone Backbone | gmx_mpi rms -f md.xtc -s 1g9m_G.pdb -o rmsd_exp.xvg -tu ns

RMSD comparsion among first conformation (rmsd.xvg), start structure (rmsd_str.xvg) and experimental structure pdb:1g9m, chain G (rmsd_exp.xvg)

RMSD comparsion between start structure (rmsd_str.xvg) and experimental structure pdb:1g9m, chain G (rmsd_exp.xvg)

RMSD comparsion among first conformation (rmsd.xvg), start structure (rmsd_str.xvg) and experimental structure pdb:1g9m, chain G (rmsd_exp.xvg)

RMSF

echo C-alpha | gmx_mpi rmsf -f md.xtc -s md.tpr -o rmsf.xvg

Dictionary of Secondary Structure for Proteins

  1. download dssp
  2. mv dssp to /usr/local/bin
  3. sudo chmod a+x /usr/local/bin/dssp
do_dssp -s md.tpr -f sys.xtc -o dssp -ver 2

Ramachandran plot

φ : C−N−CA−C ψ : N−CA−C−N

gmx_mpi rama -f md.xtc -s md.tpr -o rama.xvg

Free energy surfaces

code : generateFES.py

Principal component analysis

2D 3D

play PorcupinePlot.tcl
porcupineplot::Diff [atomselect molecular_ID "name CA"] [atomselect molecular_ID "name CA"]

Geometric clustering

echo Protein Protein | gmx_mpi cluster -f md.xtc -s md.tpr -o md_cluster.xpm -clid md_cluster.xvg -cl md_average.cluster.pdb -av

cutoff default=0.1nm

superimpose

gmx_mpi confrms -f1 ~/gp120/chains/3j70_D.pdb -f2 ~/gp120/chains/2b4c_G.pdb -o 3j70_2b4c.pdb -name