next up previous contents index
Next: Babel interface Up: VMD User's Guide Previous: Saving your work   Contents   Index

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 six molecular data file formats: PDB coordinate files, CHARMM and X-PLOR style PSF (topology) files, CHARMM and X-PLOR style DCD trajectory files, Amber structure and trajectory files (i.e. PARM and CRD), and Gromacs (i.e. GRO, G96, XTC, TRR) structure and trajectory files. These files may contain some redundant information and can be loaded in different combinations.

VMD can also load a PDB file directory from the Protein Data Bank, provided a network connection is present. Choose "pdb databank" from the list file types and enter the four-character accession code.

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). VMD supports four file formats used by Gromacs: GRO, G96, TRR and XTC. GRO and G96 files contain only structure information, including atom, residue and segment data with one coordinate set. TRR and XTC files contain only coordinate data. It should be noted that while PDB, GRO and G96 files were designed to only contain one coordinate set, multiple files can be concatenated into one larger file to create a makeshift trajectory which is recognized by VMD.

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.

Gromacs GRO and G96 files can be loaded on their own since they contain the necessary atom data and coordinates. They can also be loaded along with TRR and XTC files to obtain trajectory data.

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: VMD User's Guide Previous: Saving your work   Contents   Index