Hello,
I am going to calculate the free binding energy between two proteins using umbrella sampling. I have docked the two proteins in a complex and then fixed one of them and pulled another protein. During pulling simulation, the Center Of Mass (COM) increased from about 5.2 to 7.8 and it didn't increase more than 7.8, however I have increased the size of simulation box and pulling time. Is this increase in COM enough for calculating binding energy? Please find in attach file the pull force graph.
Thanks for your help
At the end, the two proteins should be so far away from each other that the total electrostatic interaction between them is negligible.
thank you Martin,
What shall I do to increase the distance between two proteins??
Increase the pulling force. The system should be nonperiodic. There should be no cutoff for nonbonded interactions.
thanks Martin,
here is the pulling parameters which I have used. I would appreciate if you could help me to understand, which parameters I should change.
title = Umbrella pulling simulation
define = -DPOSRES_B
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 2000000 ; 500 ps
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes ; continuing from NPT
; Single-range cutoff scheme
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = Nose-Hoover
tc_grps = Protein Non-Protein
tau_t = 1.0 1.0
ref_t = 310 310
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = Chain_A
pull_group2_name = Chain_B
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
There is 5 nm distance from protein and ligand, assuming there are no interaction between the two.
Hi Nikhil,
but the distances between two proteins have only increased from 5.2 to 7.8. I think it is not enough. I am agree with Martin's suggestion "Increase the pulling force. The system should be nonperiodic. There should be no cutoff for nonbonded interactions." but I do not know how to do it????
As per your MDP file, you are running 500 ps which is equal to 5 nm. Visualise in VMD and make sure there is sufficient distance between two proteins/molecules. How did you calcualt or obtained the value 5.2 to 7.8?
Thank you Nikhil,
In VMD the two protein do not separate completely. I have got the distances (5.2 to 7.8) after running the "trjconv" command and calculating the distances between frames (getting summary_distances.dat file).
Nikhil,
here is the last snapshot.
Just part of the protein is separated completely! The two proteins are still connected. I was unable to send the movie here