4.3 Root-mean-square fluctuation (RMSF)
In this tutorial, we analyze the root-mean-square fluctuation (RMSF). To compute the RMSF, we first use the
avecrd_analysis tool, followed by the
flccrd_analysis tool, both of which are available in the GENESIS analysis tool sets. The former computes the averaged coordinates of the selected atoms, and the latter computes the RMSF.
In this tutorial, we use the output files obtained in tutorial 1.1. (Please work on tutorial 1.1 first if you have not done it yet.) Untar
tutorial-4.3.tar.gz in the same directory as tutorial-1.1:
$ ls tutorial-1.1 $ tar -zxf ~/Download/tutorial-4.3.tar.gz $ ls tutorial-1.1 tutorial-4.3 $ cd tutorial-4.3 $ ls run.sh run1.inp run2.inp
In tutorial-1.1, we carried out an MD simulation of a small protein, BPTI, in solution. The MD simulation was performed for 500,000 steps with
crdout_period = 500 resulting in a trajectory file containing 1,000 snapshots. Here, we analyze RMSF of Cα atoms in BPTI for all snapshots.
The control file,
run1.inp, is for
avecrd_analysis. Let’s look into this file.
[INPUT] reffile = ../tutorial-1.1/1_setup/ionize.pdb # PDB file [OUTPUT] pdbfile = run1.pdb # PDB file rmsfile = run1.rms # RMSD file pdb_avefile = run1_ave.pdb # PDB file (Averaged coordinates of analysis atoms) pdb_aftfile = run1_aft.pdb # PDB file (Averaged coordinates of fitting atoms) [TRAJECTORY] trjfile1 = ../tutorial-1.1/5_production/run.dcd # trajectory file md_step1 = 500000 # number of MD steps mdout_period1 = 500 # MD output period ana_period1 = 500 # analysis period repeat1 = 1 trj_format = DCD # (PDB/DCD) trj_type = COOR # (COOR/COOR+BOX) trj_natom = 0 # (0:uses reference PDB atom count) [SELECTION] group1 = an:CA # selection group 1 [FITTING] fitting_method = TR+ROT # method fitting_atom = 1 # atom group mass_weight = YES # mass-weight is applied [OPTION] check_only = NO # (YES/NO) num_iterations = 10 # number of iterations analysis_atom = 1 # analysis target atom group
pdb_aftfile are the name of output PDB files that contain averaged coordinates of analysis atoms and averaged coordinates of fitting atoms, respectively. The averaged coordinates of the selected atoms are computed iteratively based on
Other options are the same as the input for computing the RMSD in tutorial-4.1.
The control file,
run2.inp, is for
flccrd_analysis. It is almost the same as
run1.inp except for:
[INPUT] reffile = ../tutorial-1.1/1_setup/ionize.pdb # PDB file pdb_avefile = run1_ave.pdb # PDB file (Average coordinates) pdb_aftfile = run1_aft.pdb # PDB file (Fitted Average coordinates) [OUTPUT] pcafile = run2.pca # PCA file rmsfile = run2.rms # RMSF and B-factor file vcvfile = run2.vcv # Variance-Covarience Matrix file crsfile = run2.crs # CRS file
[INPUT] section, we read
pdb_aftfile obtained from avecrd_analysis. In the
[OUTPUT] section, we specify the files to which the output data are written. RMSF is written in
pcafile is needed for the principal component analysis in tutorial-4.4.
The analysis is executed by
$ cat run.sh #!/bin/bash # set the number of OpenMP threads export OMP_NUM_THREADS=1 # perform analysis with avecrd_analysis and flccrd_analysis avecrd_analysis run1.inp | tee run1.out flccrd_analysis run2.inp | tee run2.out
Now, let’s execute this file:
$ chmod +x run.sh $ ./run.sh $ ls run.sh run1.out run1.rms run1_ave.pdb run2.inp run2.pca run2.vcv run1.inp run1.pdb run1_aft.pdb run2.crs run2.out run2.rms
run2.rms, the 4th column corresponds to RMSF in the unit of Angstrom, and the 5th column is the B-factor calculated from RMSF. This can be plotted with gnuplot:
$ gnuplot gnuplot> set xlabel "Residue number" gnuplot> set ylabel "RMSF [angstrom]" gnuplot> plot "run2.rms" using 1:4 w lp
We can see that the RMSF for the loop regions are larger than the residues forming the helix and sheet conformations, indicating that the secondary structures make the protein rigid.
Written by Kiyoshi Yagi@RIKEN Theoretical molecular science laboratory
July, 18, 2016