Notebook05: POPC/cholesterol mixture
Contents
Notebook05: POPC/cholesterol mixture¶
In this notebook, we will show you how to reconstruct hydrogens, calculate the order parameters and produce output trajectories on a POPC/cholesterol (66:34) mixture. Again, this example is based on the Berger united-atom force field.
Before going on, we advise you to get started with Notebook01 if you are not familiar with basic features of buildH and Jupyter notebooks (e.g. do you know what ! means in a Jupyter cell?).
Checking buildH activation¶
As explained in Notebook01, you should have activated buildH before launching this notebook, thus you should obtain the following when invoking buildH in a Unix terminal:
[1]:
!buildH
usage: buildH [-h] [-v] -c COORD [-t TRAJ] -l LIPID
[-lt LIPID_TOPOLOGY [LIPID_TOPOLOGY ...]] -d DEFOP
[-opx OPDBXTC] [-o OUT] [-b BEGIN] [-e END] [-igch3]
buildH: error: the following arguments are required: -c/--coord, -l/--lipid, -d/--defop
If you see this, you can go on. If not, please go to Notebook01 and see the explanations there on how to activate buildH.
Downloading the example files¶
The example shown in this Notebook are taken from a POPC/cholesterol (66:34) trajectory (84 POPC molecules and 44 cholesterol molecules) taken from the NMRlipidsIVb project. The initial source files can be found on Zenodo. For the purpose of learning, we simplified the trajectory and extracted only 25 frames (0-25 ns, one frame / ns). We also made the molecules whole with the tool
trjconv from GROMACS with the flag -pc mol. The starting gro file and the trajectory of 25 frames can be directly downloaded from the buildH repo in the directory https://github.com/patrickfuchs/buildH/tree/master/docs/Berger_POPCCHOL_test_case. Here we’ll download them with wget (recall to download all files in raw format):
[2]:
!wget https://raw.githubusercontent.com/patrickfuchs/buildH/master/docs/Berger_POPCCHOL_test_case/endCONF_OK.gro
--2021-07-07 15:17:17-- https://raw.githubusercontent.com/patrickfuchs/buildH/master/docs/Berger_POPCCHOL_test_case/endCONF_OK.gro
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1795883 (1.7M) [text/plain]
Saving to: ‘endCONF_OK.gro’
endCONF_OK.gro 100%[===================>] 1.71M --.-KB/s in 0.08s
2021-07-07 15:17:17 (22.4 MB/s) - ‘endCONF_OK.gro’ saved [1795883/1795883]
[3]:
!wget https://github.com/patrickfuchs/buildH/raw/master/docs/Berger_POPCCHOL_test_case/popcCHOL34molPER0-25ns_OK_dt1000.xtc
--2021-07-07 15:17:20-- https://github.com/patrickfuchs/buildH/raw/master/docs/Berger_POPCCHOL_test_case/popcCHOL34molPER0-25ns_OK_dt1000.xtc
Resolving github.com (github.com)... 140.82.121.3
Connecting to github.com (github.com)|140.82.121.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://raw.githubusercontent.com/patrickfuchs/buildH/master/docs/Berger_POPCCHOL_test_case/popcCHOL34molPER0-25ns_OK_dt1000.xtc [following]
--2021-07-07 15:17:20-- https://raw.githubusercontent.com/patrickfuchs/buildH/master/docs/Berger_POPCCHOL_test_case/popcCHOL34molPER0-25ns_OK_dt1000.xtc
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.108.133, 185.199.109.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2472992 (2.4M) [application/octet-stream]
Saving to: ‘popcCHOL34molPER0-25ns_OK_dt1000.xtc’
popcCHOL34molPER0-2 100%[===================>] 2.36M --.-KB/s in 0.09s
2021-07-07 15:17:21 (25.8 MB/s) - ‘popcCHOL34molPER0-25ns_OK_dt1000.xtc’ saved [2472992/2472992]
[4]:
!ls
data
endCONF_OK.gro
img
Notebook_01_buildH_calc_OP.ipynb
Notebook_02_buildH_calc_OP_outputwH.ipynb
Notebook_03_mixture_POPC_POPE.ipynb
Notebook_04_library.ipynb
Notebook_05_mixture_POPC_cholesterol.ipynb
popcCHOL34molPER0-25ns_OK_dt1000.xtc
We also need the two def files corresponding to POPC and cholesterol. They can be downloaded from the buildH repo in the directory https://github.com/patrickfuchs/buildH/tree/master/def_files (again remember to use raw files):
[5]:
!wget https://raw.githubusercontent.com/patrickfuchs/buildH/master/def_files/Berger_POPC.def
--2021-07-07 15:17:27-- https://raw.githubusercontent.com/patrickfuchs/buildH/master/def_files/Berger_POPC.def
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.111.133, 185.199.108.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2135 (2.1K) [text/plain]
Saving to: ‘Berger_POPC.def’
Berger_POPC.def 100%[===================>] 2.08K --.-KB/s in 0s
2021-07-07 15:17:27 (8.49 MB/s) - ‘Berger_POPC.def’ saved [2135/2135]
[6]:
!wget https://raw.githubusercontent.com/patrickfuchs/buildH/master/def_files/Berger_CHOL.def
--2021-07-07 15:17:30-- https://raw.githubusercontent.com/patrickfuchs/buildH/master/def_files/Berger_CHOL.def
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1275 (1.2K) [text/plain]
Saving to: ‘Berger_CHOL.def’
Berger_CHOL.def 100%[===================>] 1.25K --.-KB/s in 0s
2021-07-07 15:17:31 (5.90 MB/s) - ‘Berger_CHOL.def’ saved [1275/1275]
[7]:
!ls
Berger_CHOL.def Notebook_02_buildH_calc_OP_outputwH.ipynb
Berger_POPC.def Notebook_03_mixture_POPC_POPE.ipynb
data Notebook_04_library.ipynb
endCONF_OK.gro Notebook_05_mixture_POPC_cholesterol.ipynb
img popcCHOL34molPER0-25ns_OK_dt1000.xtc
Notebook_01_buildH_calc_OP.ipynb
Recall, the def files present on the buildH def_files directory contain all the possible (apolar) H that can be reconstructed on each lipids. The polar hydrogen of cholesterol is already present, thus it does not need to be reconstructed. buildH will let it as is, like all other non apolar H atoms.
Dealing with POPC¶
When we have a mixture of lipids, buildH cannot reconstruct hydrogens on all lipids at the same time. So we start with H reconstruction and OP calculation on POPC (we’ll focus on cholesterol later). Since Berger POPC is a supported lipid, we can launch easily buildH with the classical flags: -c for reading the initial pdb or gro file, -t for reading the trajectory, -l for specifying the type of lipid, -d for specifying the def file, -o for the output file with order
parameters, and last -opx for the output trajectory with hydrogens (recall not to put any extension, they’ll be added automatically by buildH). Importantly, when we want to output a trajectory with newly reconstructed hydrogens (option -opx), all possible H to reconstruct need to be present in the def file. This is fine since this is the case for all lipids in the def file directory of the buildH repository.
[8]:
!buildH -c endCONF_OK.gro -t popcCHOL34molPER0-25ns_OK_dt1000.xtc -l Berger_PLA -d Berger_POPC.def -o OP_POPC.out -opx traj_POPC_wH
Constructing the system...
System has 26026 atoms
Writing new pdb with hydrogens.
Writing trajectory with hydrogens in xtc file.
Dealing with frame 0 at 30000.0 ps.
Dealing with frame 1 at 31000.0 ps.
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Results written to OP_POPC.out
[9]:
!ls
Berger_CHOL.def
Berger_POPC.def
data
endCONF_OK.gro
img
Notebook_01_buildH_calc_OP.ipynb
Notebook_02_buildH_calc_OP_outputwH.ipynb
Notebook_03_mixture_POPC_POPE.ipynb
Notebook_04_library.ipynb
Notebook_05_mixture_POPC_cholesterol.ipynb
OP_POPC.out
popcCHOL34molPER0-25ns_OK_dt1000.xtc
traj_POPC_wH.pdb
traj_POPC_wH.xtc
The order parameters of POPC lipids have been written to the file OP_POPC.dat
[10]:
!head OP_POPC.out
# OP_name resname atom1 atom2 OP_mean OP_stddev OP_stem
#--------------------------------------------------------------------
gamma1_1 PLA C1 H11 0.03609 0.16545 0.01805
gamma1_2 PLA C1 H12 -0.01327 0.09031 0.00985
gamma1_3 PLA C1 H13 -0.01714 0.11162 0.01218
gamma2_1 PLA C2 H21 0.03573 0.16452 0.01795
gamma2_2 PLA C2 H22 -0.01077 0.10390 0.01134
gamma2_3 PLA C2 H23 0.00015 0.09757 0.01065
gamma3_1 PLA C3 H31 0.03542 0.16105 0.01757
gamma3_2 PLA C3 H32 -0.01826 0.09667 0.01055
A pdb traj_POPC_wH.pdb and an xtc traj_POPC_wH.xtc file have been produced with hydrogens on POPC only. So let’s check whether the POPC have hydrogens and not cholesterol (recall, here POPC residue name is PLA):
[11]:
!grep PLA traj_POPC_wH.pdb | head -20
ATOM 1 C1 PLA 1 10.670 42.050 27.850 1.00 0.00 C
ATOM 2 H11 PLA 1 10.727 41.123 27.280 1.00 0.00 H
ATOM 3 H12 PLA 1 9.962 41.929 28.670 1.00 0.00 H
ATOM 4 H13 PLA 1 11.654 42.290 28.252 1.00 0.00 H
ATOM 5 C2 PLA 1 8.900 42.780 26.440 1.00 0.00 C
ATOM 6 H21 PLA 1 8.966 41.826 25.916 1.00 0.00 H
ATOM 7 H22 PLA 1 8.564 43.552 25.748 1.00 0.00 H
ATOM 8 H23 PLA 1 8.189 42.694 27.262 1.00 0.00 H
ATOM 9 C3 PLA 1 11.120 43.130 25.800 1.00 0.00 C
ATOM 10 H31 PLA 1 11.123 42.136 25.353 1.00 0.00 H
ATOM 11 H32 PLA 1 12.130 43.389 26.117 1.00 0.00 H
ATOM 12 H33 PLA 1 10.771 43.857 25.067 1.00 0.00 H
ATOM 13 N4 PLA 1 10.220 43.140 26.970 1.00 0.00 N
ATOM 14 C5 PLA 1 10.120 44.420 27.670 1.00 0.00 C
ATOM 15 H51 PLA 1 9.433 44.285 28.506 1.00 0.00 H
ATOM 16 H52 PLA 1 9.704 45.146 26.971 1.00 0.00 H
ATOM 17 C6 PLA 1 11.420 45.010 28.230 1.00 0.00 C
ATOM 18 H61 PLA 1 12.062 44.193 28.559 1.00 0.00 H
ATOM 19 H62 PLA 1 11.177 45.647 29.081 1.00 0.00 H
ATOM 20 O7 PLA 1 12.130 45.790 27.260 1.00 0.00 O
grep: write error: Broken pipe
[12]:
!grep CHOL traj_POPC_wH.pdb | head -20
ATOM 2681 C1 CHOL 21 8.750 35.790 36.370 1.00 0.00 C
ATOM 2682 C2 CHOL 21 9.800 36.660 35.670 1.00 0.00 C
ATOM 2683 C3 CHOL 21 9.370 37.990 35.030 1.00 0.00 C
ATOM 2684 C4 CHOL 21 8.600 37.850 33.710 1.00 0.00 C
ATOM 2685 C5 CHOL 21 9.340 36.970 32.700 1.00 0.00 C
ATOM 2686 O6 CHOL 21 8.500 36.770 31.560 1.00 0.00 O
ATOM 2687 H CHOL 21 8.170 37.670 31.260 1.00 0.00 H
ATOM 2688 C8 CHOL 21 9.890 35.630 33.200 1.00 0.00 C
ATOM 2689 C9 CHOL 21 10.480 35.810 34.600 1.00 0.00 C
ATOM 2690 C10 CHOL 21 11.690 35.180 34.860 1.00 0.00 C
ATOM 2691 C11 CHOL 21 12.450 35.230 36.190 1.00 0.00 C
ATOM 2692 C12 CHOL 21 11.660 35.960 37.280 1.00 0.00 C
ATOM 2693 C13 CHOL 21 10.840 37.110 36.690 1.00 0.00 C
ATOM 2694 C14 CHOL 21 10.220 37.900 37.850 1.00 0.00 C
ATOM 2695 C15 CHOL 21 11.100 38.390 39.000 1.00 0.00 C
ATOM 2696 C16 CHOL 21 11.860 37.210 39.620 1.00 0.00 C
ATOM 2697 C17 CHOL 21 10.960 36.250 40.390 1.00 0.00 C
ATOM 2698 C18 CHOL 21 12.510 36.490 38.440 1.00 0.00 C
ATOM 2699 C19 CHOL 21 13.680 35.670 38.990 1.00 0.00 C
ATOM 2700 C20 CHOL 21 14.070 36.390 40.280 1.00 0.00 C
grep: write error: Broken pipe
Yeah that is fine! POPC has all hydrogens reconstructed, but not cholesterol (we can only see the polar hydrogen on the OH group which is natively present in a united-atom structure).
Dealing with cholesterol¶
Now that POPC have all hydrogens, we can restart from that pdb file to reconstruct the hydrogens of cholesterol. Thus we can use the flags -c with the pdb file we just generated traj_POPC_wH.pdb (Hs on POPC but cholesterol). The -t will be used with the same trajectory with H on POPC (but not POPE!) traj_POPC_wH.xtc. We output order parameters for POPE with -o. Last, -opx will produce a file with hydrogens on POPE.
[13]:
!buildH -c traj_POPC_wH.pdb -t traj_POPC_wH.xtc -l Berger_CHOL -d Berger_CHOL.def -o OP_CHOL.out -opx traj_POPC_CHOL_wH
Constructing the system...
System has 32914 atoms
Writing new pdb with hydrogens.
Writing trajectory with hydrogens in xtc file.
Dealing with frame 0 at 0.0 ps.
Dealing with frame 1 at 0.0 ps.
Dealing with frame 2 at 0.0 ps.
Dealing with frame 3 at 0.0 ps.
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Results written to OP_CHOL.out
[14]:
!ls
Berger_CHOL.def
Berger_POPC.def
data
endCONF_OK.gro
img
Notebook_01_buildH_calc_OP.ipynb
Notebook_02_buildH_calc_OP_outputwH.ipynb
Notebook_03_mixture_POPC_POPE.ipynb
Notebook_04_library.ipynb
Notebook_05_mixture_POPC_cholesterol.ipynb
OP_CHOL.out
OP_POPC.out
popcCHOL34molPER0-25ns_OK_dt1000.xtc
traj_POPC_CHOL_wH.pdb
traj_POPC_CHOL_wH.xtc
traj_POPC_wH.pdb
traj_POPC_wH.xtc
Great, we can now look at the order parameters of cholesterol:
[15]:
!head OP_CHOL.out
# OP_name resname atom1 atom2 OP_mean OP_stddev OP_stem
#--------------------------------------------------------------------
cholesterol1a CHOL C1 H11 -0.13027 0.25110 0.03785
cholesterol1b CHOL C1 H12 -0.25855 0.18820 0.02837
cholesterol1c CHOL C1 H13 0.77977 0.24458 0.03687
cholesterol3a CHOL C3 H31 -0.27535 0.24273 0.03659
cholesterol3b CHOL C3 H32 -0.28172 0.23349 0.03520
cholesterol4a CHOL C4 H41 -0.27938 0.21471 0.03237
cholesterol4b CHOL C4 H42 -0.30714 0.14779 0.02228
cholesterol5a CHOL C5 H51 -0.30473 0.20913 0.03153
And check whether POPC and POPE have all hydrogens reconstructed:
[16]:
!grep CHOL traj_POPC_CHOL_wH.pdb | head -20
ATOM 2681 C1 CHOL 21 8.750 35.790 36.370 1.00 0.00 C
ATOM 2682 H11 CHOL 21 8.249 36.375 37.141 1.00 0.00 H
ATOM 2683 H12 CHOL 21 9.238 34.929 36.827 1.00 0.00 H
ATOM 2684 H13 CHOL 21 8.017 35.447 35.640 1.00 0.00 H
ATOM 2685 C2 CHOL 21 9.800 36.660 35.670 1.00 0.00 C
ATOM 2686 C3 CHOL 21 9.370 37.990 35.030 1.00 0.00 C
ATOM 2687 H31 CHOL 21 10.267 38.580 34.839 1.00 0.00 H
ATOM 2688 H32 CHOL 21 8.733 38.517 35.740 1.00 0.00 H
ATOM 2689 C4 CHOL 21 8.600 37.850 33.710 1.00 0.00 C
ATOM 2690 H41 CHOL 21 7.627 37.405 33.917 1.00 0.00 H
ATOM 2691 H42 CHOL 21 8.462 38.841 33.277 1.00 0.00 H
ATOM 2692 C5 CHOL 21 9.340 36.970 32.700 1.00 0.00 C
ATOM 2693 H51 CHOL 21 10.245 37.528 32.460 1.00 0.00 H
ATOM 2694 O6 CHOL 21 8.500 36.770 31.560 1.00 0.00 O
ATOM 2695 H CHOL 21 8.170 37.670 31.260 1.00 0.00 H
ATOM 2696 C8 CHOL 21 9.890 35.630 33.200 1.00 0.00 C
ATOM 2697 H81 CHOL 21 10.667 35.280 32.521 1.00 0.00 H
ATOM 2698 H82 CHOL 21 9.084 34.898 33.237 1.00 0.00 H
ATOM 2699 C9 CHOL 21 10.480 35.810 34.600 1.00 0.00 C
ATOM 2700 C10 CHOL 21 11.690 35.180 34.860 1.00 0.00 C
grep: write error: Broken pipe
[17]:
!grep PLA traj_POPC_CHOL_wH.pdb | head -20
ATOM 1 C1 PLA 1 10.670 42.050 27.850 1.00 0.00 C
ATOM 2 H11 PLA 1 10.730 41.120 27.280 1.00 0.00 H
ATOM 3 H12 PLA 1 9.960 41.930 28.670 1.00 0.00 H
ATOM 4 H13 PLA 1 11.650 42.290 28.250 1.00 0.00 H
ATOM 5 C2 PLA 1 8.900 42.780 26.440 1.00 0.00 C
ATOM 6 H21 PLA 1 8.970 41.830 25.920 1.00 0.00 H
ATOM 7 H22 PLA 1 8.560 43.550 25.750 1.00 0.00 H
ATOM 8 H23 PLA 1 8.190 42.690 27.260 1.00 0.00 H
ATOM 9 C3 PLA 1 11.120 43.130 25.800 1.00 0.00 C
ATOM 10 H31 PLA 1 11.120 42.140 25.350 1.00 0.00 H
ATOM 11 H32 PLA 1 12.130 43.390 26.120 1.00 0.00 H
ATOM 12 H33 PLA 1 10.770 43.860 25.070 1.00 0.00 H
ATOM 13 N4 PLA 1 10.220 43.140 26.970 1.00 0.00 N
ATOM 14 C5 PLA 1 10.120 44.420 27.670 1.00 0.00 C
ATOM 15 H51 PLA 1 9.430 44.290 28.510 1.00 0.00 H
ATOM 16 H52 PLA 1 9.700 45.150 26.970 1.00 0.00 H
ATOM 17 C6 PLA 1 11.420 45.010 28.230 1.00 0.00 C
ATOM 18 H61 PLA 1 12.060 44.190 28.560 1.00 0.00 H
ATOM 19 H62 PLA 1 11.180 45.650 29.080 1.00 0.00 H
ATOM 20 O7 PLA 1 12.130 45.790 27.260 1.00 0.00 O
grep: write error: Broken pipe
Conclusion¶
In this notebook, we showed you how to use buildH on a mixture of POPC/cholesterol lipids. buildH has to be launched for each lipid separately. If a trajectory with all hydrogens on all lipids is wanted, one has to produce intermediate trajectories at each step. In the figure below is shown a snapshot with all the reconstructed hydrogens on cholesterol molecules (POPC and water are not shown for clarity, image rendered with VMD).
