The present version of MobyWat accepts four types of structural input files. File types are automatically recognized by extensions of file names.
1.1. Binary trajectory file (*.xtc)
The xtc format is a portable binary format which can store trajectories in an efficient, compressed form. It uses the xdr routines for writing and reading data. Xtc files can be produced by e.g. MD package GROMACS. Note that xtc files contain only spatial coordinates x,y,z of all atoms of all frames of the trajectory. Similarly to other programs reading binary trajectories, MobyWat also requires the definition of atom types in a separate PDB-type topology file. The topology file must contain the same number of atoms in the same order as one frame. Production of such a topology file can be easily done along with the production of the xtc file in GROMACS.
1.2 Separate PDB files (*.pdb)
For compatibility with any MD packages, MobyWat can also read a trajectory as a series of individual frames stored in standard PDB files. Obviously, the frames must have the same number of atoms in the same order. The files must have a sequential naming such as system_i.pdb, where the use of _i.pdb part of the file names is mandatory (i=x, x+1,x+2,…,y in MobyWat command line switch –n x-y, see also Input ranges). Note, that topology file is not used for PDB files as they have all necessary information for MobyWat. For additional information on PDB files, please visit the Protein Databank web site.
1.3 NMR-type PDB files (*.pdb)
Instead of a series of PDB files a trajectory can be also stored in a single PDB file and frames can be handled as NMR models within the same file. MobyWat automatically recognizes NMR-type PDB files if the file name contains the token mdl in a form such as system_mdl.pdb. Note, that in NMR-type PDB files the models (=frames) are defined using MODEL and ENDMDL tokens and model serial numbers specified after MODEL must be within the x-y range of switch –n x-y of MobyWat command line (see also Input ranges). For additional information on NMR-type PDB files, please visit the corresponding Protein Databank page.
It is important to note that storage of trajectories in PDB files may require much disk space, and therefore, xtc binary files can be recommended for routine use. However, MobyWat can also read PDB inputs described above to ensure compatibility with any MD software packages. When reading PDB input files MobyWat automatically converts the trajectories into xtc format and also creates a topology file used for subsequent calculations.
1.4 Binary pool waters file (*.plw)
MobyWat stores pool waters of the trajectory in a non-portable binary file which is automatically created as a first step of processing input files described in Sections 1.1-3. The file contains pool waters only from frames specified by the x-y range of switch –n x-y of MobyWat command line. MobyWat also produces a pool information file (*.pli) along with the plw file for future use. The pli file contains information such as dmax specifying the pool. As creation of water pools from the trajectory file may take considerable time for large systems, pool waters file can be useful if re-running of a prediction/analysis is required by the user e.g. for experimenting with various clustering schemes, tolerances, etc. Importantly, dmax cannot be changed in such repeated runs as it defines the pool, itself. For information on the structure of pool waters file, please refer to Program details.
MobyWat produces binary files and text files and all of them are marked with O_ in the beginning of the file name. Files xtc, plw, and pdb were described in Section 1. In other text files such as lst and txt additional information on e.g. clustering, RMSD, number of interface waters per frame, etc. are printed. MobyWat also creates a log file with details on input/output information.