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Loading A Molecule

   

The Files form is the primary means for loading a new molecule into VMD from one or more data files. VMD natively understands five molecular data  file formats: PDB coordinate files, CHARMM and X-PLOR style PSF (topology)     files, CHARMM and X-PLOR style DCD trajectory files, and Amber structure and trajectory files (i.e. PARM and CRD). These files contain some redundant information and can be loaded in different combinations.

The PDB file contains data about the atom, residue, and segment names, the occupancy and beta factor, and one coordinate set. The PSF and PARM files list the atom, residue, and segment names, the residue type, atomic mass and charge, and the bond connectivity. The DCD and CRD files contain only the atomic coordinates over multiple frames (timesteps).

When VMD loads a file it requires information about atom names and coordinates and tries to fill in the rest. Since the PDB file contains all this information, it does not need to be loaded with any other data files. However, the PDB file doesn't contain the atom types, masses, and charges, so these are guessed.

A PSF file does not contain coordinate information so it must be loaded along with a PDB or DCD file. If a PDB and PSF are given there is no missing data and VMD makes no assumptions. If a PSF and DCD are given then only the chain identifier and occupancy and beta values are missing so they are given a default value.

A PARM file is similar to a PSF in that it too contains no coordinate information. It must be loaded along with an CRD trajectory file. If a PARM and CRD file are loaded together, then only the segname and chain ID for the atoms are left blank. VMD fills in the remaining fields explicitly, making no assumptions.

A CRD or DCD file can be specified along with the PDB, in which case the PDB file will be read as normal, and then coordinate sets are read from the DCD or CRD until the end of the file is reached.

Additional coordinates from a PDB, CRD, or DCD file can be appended to the current coordinate set using the Edit form.




next up previous contents index
Next: Babel interface Up: No Title Previous: External Interfaces

Justin Gullingsrud
Tue Apr 6 09:22:39 CDT 1999