load_hbond function

Loading hydrogen bond data

This function loads hydrogen bond information from a text file and stores it in a table. See functions hbond() and hbond_ts() for usage of the return value.

load_hbond( path,
            GROMACShbondlogfile = NA,
            mdEngine = "GROMOS" )

Arguments

• path: Specifies the path of the text input file.
• GROMACShbondlogfile: Additional file path required in case GROMACS format is specified.
• mdEngine: Argument distinguishes between input formats based on the molecular dynamics engine used. Currently available: "GROMOS", "GROMACS" and "AMBER". Note, that load_hbond() is able to load both summary and time-series data for the AMBER simulation package.

Returns

Returns a table, where the hydrogen bonds are stored in a row-wise fashion and the columns hold the following information (note, that information not available e.g. because the MD analysis tool output does not provide it, is represented by NA values):

• hbondID The identifier number of the hydrogen bonds (if not given by the input, they are numbered ascendingly).
• resDonor Number of the donor residue.
• resDonorName Name of the donor residue.
• resAcceptor Number of the acceptor residue.
• resAcceptorName Name of the acceptor residue.
• atomDonor Number of atom, that is the hydrogen bond donor.
• atomDonorName Name of atom, that is the hydrogen bond donor.
• atomH Number of atom (proton) that is forming the hydrogen bond.
• atomAcceptor Number of atom, that is the hydrogen bond acceptor.
• atomAcceptorName Name of atom, that is the hydrogen bond acceptor.
• percentage Number between 0 and 100 in percent representing the occurence rate of a particular hydrogen bond over the trajectory.

Examples

# GROMOS
load_hbond( system.file( "extdata/hbond_example.txt.gz", package = "MDplot" ) )

# GROMACS
load_hbond( system.file( "extdata/hbond_ts_example_GROMACS.xpm.gz",
                         package = "MDplot" ),
            system.file( "extdata/hbond_example_GROMACS.txt.gz",
                         package = "MDplot" ),
            mdEngine = "GROMACS" )

# AMBER (summary)
load_hbond( system.file( "extdata/hbond_example_AMBER.txt.gz",
            package = "MDplot" ), mdEngine = "AMBER" )

# AMBER (time-series)
load_hbond( system.file( "extdata/hbond_ts_example_AMBER.txt.gz",
            package = "MDplot" ), mdEngine = "AMBER" )

Author(s)

Christian Margreitter