xpl2lis

xpl2lis 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 ($IFFIHOME/share/iffi/units.def).
Optionally, you can provide a file with constraint definitions ($IFFIHOME/share/iffi/shake.def).

Usage:

   xpl2lis.plumed.mpi <pdb> <psf> <units> <param 1> <param 2> [-s <shake> ]

xpl2lis 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.

xpl2lis will be superseeded by [xpl2iph] starting from version 1.4.