Package: buildh
buildHBuild hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parametersFeaturesbuildHcan :Reconstruct hydrogens from aunited-atomstructure 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.buildHworks in two modes :A slow mode when an output trajectory (in xtc format) is requested by
the user. In this case, the whole trajectory including newly built
hydrogens are written to this trajectory.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, runningbuildHon a trajectory of 2500 frames with 128 POPC (without trajectory output) takes ~ 7' on a single core Xeon @ 3.60GHz.RequirementsPython >= 3.6 is mandatory for running buildH.buildHis written in Python 3 and needs the modules numpy, pandas, MDAnalysis and Numba.InstallationPipA simple installation with pip will do the trick:python3 -m pip install buildhAll dependencies (modules) will be installed automatically by pip.CondabuildHis also available through theBiocondachannel:conda install buildh -c bioconda -c conda-forgeMore details on installationhere.For installing a development version, seehere.Running buildHOnce installed, a simple invocation of thebuildHcommand will run the program ($represents the Unix prompt):$ buildH
usage: 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/--defopThe minimal command for runningbuildHcan resemble this:$ buildH -c start_128popc.pdb -t popc0-25ns_dt1000.xtc -l Berger_POPC -d Berger_POPC.defThe different arguments mean the following:-c start_128popc.pdbis a pdb file with 128 POPC molecules,-t popc0-25ns_dt1000.xtcis a trajectory with 25 frames,-l Berger_POPCindicates the united-atom force field and the type of lipid to be analyzed,-d Berger_POPC.defindicates 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.outOther 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).buildHtakes 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 liketrjconvin GROMACS with flag-pbc mol).InvokingbuildHwith the-hflag will display some help to the screen and tell which lipids are supported.$ buildH -h
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]
[...]
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.DocumentationThe full documentation is available atRead the Docs.ContributorsHubert SantuzAmélie BâclePierre PoulainPatrick FuchsLicensebuildHis licensed under theBSD License.ContributingIf you want to report a bug, request a feature, or propose an improvement use theGitHub issue system.Please, see also theCONTRIBUTINGfile.Note that this project is released with aContributor Code of
Conduct. By participating in this project you
agree to abide by its terms. See theCODE_OF_CONDUCTfile.CitingbuildHIf you usebuildHfor 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.03521BSD 3-Clause LicenseCopyright (c) 2019, Patrick FUCHS
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