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lammps/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt
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# Description:
# This example shows how to put a protein (inclusion) in a
# lipid bilayer mixture composed of two different lipids (DPPC and DLPC).
# The DPPC lipid model is described here:
# G. Brannigan, P.F. Philips, and F.L.H. Brown,
# Physical Review E, Vol 72, 011915 (2005)
# The protein model is described here:
# G. Bellesia, AI Jewett, and J-E Shea,
# Protein Science, Vol19 141-154 (2010)
# The new DLPC model is a truncated version of DPPC,
# (Its behaviour has not been rigorously tested.)
# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to
# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293
# Note:
# This example may require additional features to be added to LAMMPS.
# If LAMMPS complains about an "Invalid pair_style", then copy the code
# in the "additional_lammps_code" directory into your LAMMPS "src" directory
# and recompile LAMMPS.
import "CGLipidBr2005.lt"
using namespace CGLipidBr2005
# The "= new random" syntax chooses one of several molecules at random
lipids = new random([DPPC, DLPC], [0.5,0.5], 1234) #"1234"=random_seed
[13].move(7.5, 0, 0)
[15].move(3.75, 6.49519, 0) # <-- hexagonal lattice
[2].rot(180, 1, 0, 0) # <-- 2 monolayers
# Move all the lipds up to the center of the box
lipids[*][*][*].move(0,0,75.0)
# Although this patch of lipids is not square or rectangular, (it looks
# like a parallelogram), this is no longer the case after rectangular
# periodic boundary conditions are applied. (Check by visualising in VMD.)
write_once("Data Boundary") {
0 97.5 xlo xhi
0 97.42785792 ylo yhi
0 150.0 zlo zhi
}
# A note on geometry:
# We want to create a bilayer arranged in a hexagonal lattice consisting of
# 15 rows (each row is aligned with the x-axis)
# 13 columns (aligned at a 60 degree angle from the x axis)
# The lattice spacing is 7.5 Angstroms.
# When wrapped onto a rectangular box, the dimensions of the system are:
# 13 * 7.5 Angstroms in the X direction
# 15 * 7.5*sqrt(3)/2 Angstroms in the Y direction
# ------------------- protein inclusion ---------------------
import "1beadProtSci2010.lt"
using namespace 1beadProtSci2010
protein = new 4HelixInsideOut
protein.move(45.0, 25.98076211, 75.0)
# Delete a hole in the membrane to create space for the protein.
delete lipids[4][2][*]
delete lipids[6][2][*]
delete lipids[3-6][3][*]
delete lipids[3-5][4][*]
delete lipids[2-5][5][*]
delete lipids[2][6][*]
delete lipids[4][6][*]
# Note: All atom types must include the full path (the name of
# the namespace which defined them as well as the atom type name).
# (This is because we are no longer inside that namespace.)
write_once("In Settings") {
# -----------------------------------------------------------
# -------- interactions between protein and lipids ----------
# -----------------------------------------------------------
# Interactions between the protein and lipid atoms are usually
# determined by mixing rules. (However this is not possible some
# for atoms, such as the "int" atoms in the lipid model which
# interact using -1/r^2 attraction.) Mixing rules do not make
# sense for these atoms so we must explicitly define their
# interaction with all other atoms.
# We want the hydrophobic interactions between hydrophobic residues in
# the protein and beads the interior of the lipid to be energetically
# similar to the attractive interactions between the lipid tails.
#
# Note: I made the width of the outward-facing protein beads slightly larger
# ("12.5") whenever they interact with the "tail" beads in each lipid
# (in order to make the protein wider there).
# This hopefully relieves some of the internal negative pressure in the center
# of the bilayer which can otherwise rip apart the protein or suck it into
# the bilaer. (This is a hack, and I'm not sure if it is necessary.
# For different protein or lipid models, you probably don't need this.)
#
# i j pairstylename eps sig K L
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
# To help keep the protein from tilting 90 degrees and burying itself
# within the lipid bilayer, we make the turn regions at either
# end of the protein (strongly) attracted to the head groups
# of the lipid. (In reality, they would probably be attracted
# to the water as well.)
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
# All other interactions between proteins and lipids are steric.
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
# -----------------------------------------------------------
# -------- Modifications to the protein model: --------------
# -----------------------------------------------------------
#
# Turn off attraction between the hydrophobic "@atom:sH" beads:
# (These beads are located in the outside of a trans-membrane protein.)
pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0
# (Why: These beads are only attracted to
# each other in an aqueous environment)
# ... and
# Turn ON attraction between the hydrophilic "@atom:sL" beads.
# (These beads are located in the interior of a trans-membrane protein.)
pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
# Why?
# In reality, polar groups in the interior of trans-membrane
# proteins do form hydrogen bonds with each other. This was
# absent from the original protein model because, in an aqueous
# environment, these groups preferentially interact with the water.
#
# Why is this necessary?
# Shouldn't attraction between lipid tails and the protein create
# an effective force which brings the hydrophilic beads together?
# (similar to the hydrophobic effect, but in reverse?).
# Answer:
# Unlike an aqueous environment (~zero pressure, or +1atm), there is
# a large negative pressure in the interior of some bilayer membrane
# models (such as this one). Without some kind of direct attraction
# between interior residues, the protein will get pulled apart.
# (Perhaps the attractive force I am using is too strong?)
}
# Finally, we must combine the two force-field styles which were used for
# the coarse-grained lipid and protein. To do that, we write one last time
# to the "In Init" section. When reading the "Init" section LAMMPS will
# read these commands last and this will override any earlier settings.
write_once("In Init") {
# -- These styles override earlier settings --
units real
atom_style full
# (Hybrid force field styles were used for portability.)
bond_style hybrid harmonic
angle_style hybrid cosine/delta harmonic
dihedral_style hybrid fourier
improper_style none
pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15
pair_modify mix arithmetic
special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
}
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