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Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters

buildH can :

• Reconstruct hydrogens from aunited-atom structure file (pdb, gro) or trajectory (e.g. xtc).
• Calculate the order parameters based on the reconstructed hydrogens.
• Write new structure trajectory files with the reconstructed hydrogens.

buildH works in two modes :

1. A slow mode when an output trajectory (in xtc format) is requested bythe user. In this case, the whole trajectory including newly builthydrogens are written to this trajectory.
2. A fast mode without any output trajectory.

In both modes, the order parameters are calculated. All calculations are accelerated withNumba. As a CPU cost indication, runningbuildH on a trajectory of 2500 frames with 128 POPC (without trajectory output) takes ~ 7' on a single core Xeon @ 3.60GHz.

Python >= 3.6 is mandatory for running buildH.

buildH is written in Python 3 and needs the modules numpy, pandas, MDAnalysis and Numba.

A simple installation with pip will do the trick:

python3 -m pip install buildh

All dependencies (modules) will be installed automatically by pip.

buildH is also available through theBioconda channel:

conda install buildh -c bioconda -c conda-forge

More details on installationhere.

For installing a development version, seehere.

Once installed, a simple invocation of thebuildH command will run the program ($ represents the Unix prompt):

$ buildHusage: buildH [-h] -c COORD [-t TRAJ] -l LIPID [-lt LIPID_TOPOLOGY [LIPID_TOPOLOGY ...]] -d DEFOP              [-opx OPDBXTC] [-o OUT] [-b BEGIN] [-e END] [-pi PICKLE] [-igch3]buildH: error: the following arguments are required: -c/--coord, -l/--lipid, -d/--defop

The minimal command for runningbuildH can resemble this:

$ buildH -c start_128popc.pdb -t popc0-25ns_dt1000.xtc -l Berger_POPC -d Berger_POPC.def

The different arguments mean the following:-c start_128popc.pdb is a pdb file with 128 POPC molecules,-t popc0-25ns_dt1000.xtc is a trajectory with 25 frames,-l Berger_POPC indicates the united-atom force field and the type of lipid to be analyzed,-d Berger_POPC.def indicates what C-H are considered for H building and order parameter calculation (the structure and trajectory files can be foundhere). The def file can be foundhere. The final order parameters averaged over the trajectory will be written to the default output nameOP_buildH.out

Other detailed examples and Jupyter Notebooks can be found in the documentation atRead the Docs.

Important: sometimes, when performing MD, some molecules are split over periodic boundary conditions (PBC).buildH takes as input whole structures (pdb, gro, xtc, etc.). If broken molecules are supplied, it will most likely generate nonsense results. So it is up to the user to take care of making molecules whole before runningbuildH (e.g. by using a tool liketrjconv in GROMACS with flag-pbc mol).

InvokingbuildH with the-h flag will display some help to the screen and tell which lipids are supported.

$ buildH -husage: 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][...]The list of supported lipids (-l option) are: Berger_CHOL, Berger_DOPC, Berger_DPPC, Berger_POP, Berger_POPC, Berger_PLA, Berger_POPE, Berger_POPS, CHARMM36UA_DPPC, CHARMM36UA_DPUC, CHARMM36_POPC, GROMOS53A6L_DPPC, GROMOSCKP_POPC, GROMOSCKP_POPS. More documentation can be found at https://buildh.readthedocs.io.

The full documentation is available atRead the Docs.

• Hubert Santuz
• Amélie Bâcle
• Pierre Poulain
• Patrick Fuchs

buildH is licensed under theBSD License.

If you want to report a bug, request a feature, or propose an improvement use theGitHub issue system.

Please, see also theCONTRIBUTING file.

Note that this project is released with aContributor Code ofConduct. By participating in this project youagree to abide by its terms. See theCODE_OF_CONDUCT file.

If you usebuildH for your research, please cite :

Santuz et al., (2021). buildH: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters. Journal of Open Source Software, 6(65), 3521, https://doi.org/10.21105/joss.03521