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lammps/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt
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1beadProtSci2010_variations.lt
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### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ##
### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE##
#
# This file defines a family of coarse-grained protein models used in:
# G. Bellesia, AI Jewett, and J-E Shea,
# Protein Science, Vol19 141-154 (2010)
#
# Strategy:
#
#1) First I'll define some building blocks (A16, B16, T3)
# which are helices, sheets and turns of a predetermined length)
import "1beadProtSci2010.lt"
# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below
#
#2) Then I'll copy and paste them together to build
# a 4-helix bundle or a 4-strand beta-barrel.
1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier
# This way we don't have to start from scratch. We can
# use all the atom types and angle settings defined earlier
# B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each)
B16 {
# AtomID MoleculeID AtomType Charge X Y Z
write('Data Atoms') {
$atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0
$atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8
$atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6
$atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4
$atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2
$atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0
$atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8
$atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6
$atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4
$atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2
$atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0
$atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8
$atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6
$atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4
$atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2
$atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0
}
write('Data Bonds') {
$bond:b1 @bond:../backbone $atom:a1 $atom:a2
$bond:b2 @bond:../backbone $atom:a2 $atom:a3
$bond:b3 @bond:../backbone $atom:a3 $atom:a4
$bond:b4 @bond:../backbone $atom:a4 $atom:a5
$bond:b5 @bond:../backbone $atom:a5 $atom:a6
$bond:b6 @bond:../backbone $atom:a6 $atom:a7
$bond:b7 @bond:../backbone $atom:a7 $atom:a8
$bond:b8 @bond:../backbone $atom:a8 $atom:a9
$bond:b9 @bond:../backbone $atom:a9 $atom:a10
$bond:b10 @bond:../backbone $atom:a10 $atom:a11
$bond:b11 @bond:../backbone $atom:a11 $atom:a12
$bond:b12 @bond:../backbone $atom:a12 $atom:a13
$bond:b13 @bond:../backbone $atom:a13 $atom:a14
$bond:b14 @bond:../backbone $atom:a14 $atom:a15
$bond:b15 @bond:../backbone $atom:a15 $atom:a16
}
} # B16
# ----- Now build larger molecules using B16 and T3 -------
4SheetBarrel {
sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0)
sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0)
sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0)
sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0)
turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6)
turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4)
turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6)
write('Data Bonds') {
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16
}
create_var { $mol } # molecule ID number shared by all atoms in this protein
}
# Below I define several alternate conformations of the"4HelixBundleInsideOut"
# molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however.
4HelixBundle {
helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4)
helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8)
helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2)
helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6)
write('Data Bonds') {
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
}
turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2)
turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9)
turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4)
create_var { $mol } # molecule ID number shared by all atoms in this protein
} # 4HelixBundle
# --- alternate conformations (same molecule) ----
# In the following version, the helices are oriented in a similar way,
# but they are separated a little further away from eachother.
4HelixBundleLoose {
helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0)
helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0)
helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0)
helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0)
turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4)
turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8)
turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4)
write('Data Bonds') {
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
}
create_var { $mol } # molecule ID number shared by all atoms in this protein
}
# In following version, the helices are oriented in a similar way,
# but they are separated a little further away from eachother.
4HelixInsideOutLoose {
helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0)
helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0)
helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0)
helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0)
turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8)
turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2)
turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8)
write('Data Bonds') {
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
}
create_var { $mol } # molecule ID number shared by all atoms in this protein
} # 4HelixInsideOutLoose
# In the following version, the 4 helices are arranged next to each other,
# side-by-side, in a planar conformation (instead of a compact bundle).
4HelixPlanar {
helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0)
helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0)
helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0)
helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0)
turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8)
turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8)
turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8)
write('Data Bonds') {
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
}
create_var { $mol } # molecule ID number shared by all atoms in this protein
} # 4HelixPlanar
# -------- Minor coordinates adjustment: -----------
# Those coordinates in the commands above are a little too large.
# To make it easier to type them in, I was using sigma=6.0 Angstroms.
# Instead, here I'll try using sigma=4.8 Angstroms. 4.8/6.0 = 0.8)
4SheetBarrel.scale(0.8)
4HelixBundle.scale(0.8)
4HelixBundleLoose.scale(0.8)
4HelixInsideOutLoose.scale(0.8)
4HelixPlanar.scale(0.8)
# Note: "scale()" only effects the initial coordinates of
# the molecule, not the force field parameters.
# (If you plan to minimize the molecule, you don't need to
# be so careful about the initial coordinates. In that case,
# you don't have worry about "scale()". Feel free to remove.)
} # 1beadProtSci2010 (namespace)
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