xpl2iph

xpl2iph is used to generate input files for the iffi MD engine. For a particular system it requires the coordinates in the protein data base format (.pdb) and the topology
in the charmm protein structure file (.psf) format. You can built these files, for example,
with tools provided by the visual molecular dynamics (vmd) package. The parameters for the bonded and nonbonded potentials have to be provided by one or more charmm parameter files. These can be obtained from the MacKerell Group. xpl2lis supports the current charmm file format including CMAP potentials. Furthermore, you need the iphigenie specific file defining the structural units (charge groups). A file covering the typical residues solvated proteins is supplied with this distribution ($IFFIHOME/share/iffi/units.def).
Furthermore, constraint definitions for residues and molecules can be speciefied (default: $IFFIHOME/share/iffi/shake.def).

Usage:
  xpl2iph.gnu.seq [options]
  Options:
     -h  --help   Show this message
     -b  --pdb    <pdf-file>[@n] 
     -f  --psf    <pdf-file>[@n] 
     -u  --units  <units-file> (def: units.def)
     -s  --shake  <shake-file> (def: shake.def)
     -c  --charmm <param-file> 
     -p  --pmmii  <pmmii-file>

All file options can be given multiple times. Appending @n to pdb and psf files is the same as using n-times the -b or -f option with the same file. xpl2iph will concatenate these files in order of appearance on the command line with the appropriate offset for the atom indices. If you use these multifile options, make sure that the atom order of the concatenated pdb and psf files is the same! If input files cannot be accessed from the working directory xpl2iph looks the appropriate subdirectories of $IFFIHOME/share. This path can be overridden by the environment variable $IFFISHARE.
xpl2iph writes a log file that shoud be checked. The input files for iffi are written in the iph directory and a template for the run control files ctl.xml is created the working directory.

xpl2iph superseeds xpl2lis starting from version 1.4.