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lammps/tools/moltemplate/examples/CG_membrane_examples/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.
# (In the future moltemplate will be able to avoid occlusion automatically.)
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][*]
# -------- interactions between protein and lipids ----------
# 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 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.
# i j pairstylename eps sig K L
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
# We want the interactions between hydrophobic residues and atoms in
# the interior of the lipd to be energetically similar to the attractive
# interactions between hydrophobic residues. (See 1beadProtSci2010.)
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1
# We also add an artificial attractive interaction between the
# turn residues of the protein and the lipid head groups in
# order to keep the protein upright. Probably not necessary.
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1
# All other interactions between proteins and lipids are steric.
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
# Add a weak attractive interaction between hydrophilic "sL" beads
# (Whose strength mimics the strength of interaction between tail beads
# in the lipid. This was absent from the original protein model.
# However without some kind of weak attraction between residues,
# the negative pressure in the interior of the bilayer membrane
# allways pulls the protein apart. Recall that in the membrane,
# the hydrophobic beads in the protein will face outwards towards the lipid
# tails leaving the hydrophilic amino acids of the protein in the interior.
# In reality, these polar groups form hydrogen bonds with each other.)
pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.3286 7.5 0.4 -1
# However these hydrophilic amino acids are not attrected to
# the bilayer interior.
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
}
# 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 class2
improper_style none
pair_style hybrid table linear 1001 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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