Brief instruction for PMF
analysis of self-association of TM helical peptides.
This
instruction illustrates how we analyzed the PMF profile of interaction between
two TM peptides, using as an example 'CG-WALP19-oc' (the set #19b of our 2014
paper "Potential
of mean force analysis of the self-association of leucine-rich
transmembrane α-helices: difference between atomistic
and coarse-grained simulations" by M. Nishizawa and K. Nishizawa (2014) J Chem Phys ).
1. Please get
a computer that runs Gromacs 4.x ready.
Download the zip file or
its content (eight files): .gro, .top, .itp, .itp (Martini-v2.1),
.itp
(Martini-sol), .ndx, pre.mdp and run.mdp (named
cg_w22.mdp) files. ( When you
publish your results obtained using the Martini itp
files above, please cite the Martini paper(s) by Marrink
and coworkers. )
2. First, initial coordinates (gro files) that have various inter-helical distances have
to be prepared. Do 'grompp' using the pre.mdp file and the above listed gro, top, itp files. Then, do 'mdrun'
the obtained tpr file, which is a steered dynamics
run that gradually brings the helices closer to each other ( from 2.2 nm to 0.4
nm).
3. Do trjconv
against the .trr file obtained in 2. For this trjconv,
we suggest to use " -sep -skip 10". This generates a series of gro files with inter-helical distances of 2.1nm, 2.0 nm,
1.9nm,.. and so on. Please rename
the .gro files, including the number reflecting
inter-helical distance in the name, like , such as, walp19_21.gro, walp19_20.gro, walp19_19.gro,... etc. For each of these gro files. do the following 4 and 5.
4. To make .tpr
file, do grompp
(e.g., grompp -f
cg_22w.mdp -c walp19_21(and so on).gro -n
*.ndx
-p *.top -o walp19_21(and so on).tpr
). Of course, the 'pull_init1'
value in the run.mdp file has to be altered in advance appropriately; this
restrains the inter-helical distance (in nm) by the umbrella harmonic
potential.
5. Run the tpr. (
e.g., mdrun -deffnm
walp19_21(and so on).tpr -px pullx_walp19_21(and so on).xvg -pf
pullf_walp19_21(and so on).xvg ) . If the peptide has popped out the octane
slab, repeat the 4 and 5 with another set of the initial velocities.
6. Create a file named ' tpr-files_walp19.dat ',
which is a list file of walp19_21(and so on).tpr. Also, create pullf-files_walp19.dat, which is a list file of pullf_walp19_21(and so
on).xvg . To do so, enter one file name per line
just like,
walp19_21.tpr
walp19_20.tpr
walp19_19.tpr
....
.
Then do g_wham. (e.g., g_wham -it
tpr-files_walp19.dat
-if pullf-files_walp19.dat -o
profile.xvg -hist hist.xvg -unit kJ
-b 500000 -temp 323
-min 0.5 -max 2.3 )
Actually, by modifying the step 3, we generated and used 23
windows (inter-helical distances) in total: 0.6, 0.7, 0.75, 0.8, 0.85, 0.9,
0.95, 1.0,1.05, 1.1, 1.15, 1.2, 1.25, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0,
2.1, 2.2 nm.
For this set, we obtained a PMF curve with a depth of ~ 28.5 kJ/mol.