Next: CHARMM/X-PLOR to MMTK Up: Trajectory conversion Previous: Trajectory conversion Contents

###
Amber to MMTK

This converter allows the conversion from a NetCDF trajectory generated with Amber 9 or 10 [26] to a MMTK NetCDF trajectory (unfortunately, both NetCDF files do not follow the same convention). For version of Amber lower than 9, Amber provides some tools for the conversion to Amber NetCDF trajectories. Pressing the Amber NetCDF to MMTK menubutton, the dialog shown in figure 4.4 will pop up.

Figure 4.4: The Amber to MMTK converter dialog.

To perform the conversion, the following input fields must be filled:

- PDB input file
  Format: string
  Default: None
  Description: a PDB file of the system must be provided for the conversion. This file is necessary to build up the MMTK universe related to the MMTK trajectory.

- Amber NetCDF input file
  Format: string
  Default: None
  Description: the Amber 9 or 10 NetCDF trajectory file that contains all the trajectory frames.

- Time step (in ps)
  Format: strictly positive float
  Default: 1.0
  Description: the time step in ps between two consecutive frames of the Amber NetCDF trajectory. You have to provide this information because it is not contained in the Amber NetCDF trajectory file.

- MMTK NetCDF output file
  Format: string
  Default: None
  Description: the name of the MMTK NetCDF trajectory that will be written. Once, an Amber NetCDF file has been loaded, a default name for the MMTK NetCDF output file will be proposed. This default name will be file_mmtk.nc if file.nc is the Amber NetCDF trajectory file name.

Next: CHARMM/X-PLOR to MMTK Up: Trajectory conversion Previous: Trajectory conversion Contents