Writing PDB files with TER cards in VMD
Patched lines © 2010 Universitat Pompeu Fabra. Author: Toni Giorgino - Draft version (Jul/2010)
This plugin allows VMD to write PDB files with embedded TER cards. The PDB standard mandates the presence of 'TER' cards between unconnected fragments. Most software does not need them, but other (most notably AmberTools' tleap) does.
The plugin relies on connectivity information, so a .psf or .prmtop file must be loaded beforehand. It works in the animate write command and in the GUI as well.
Notes. The plugin is write-only (the normal PDB plugin reads TER cards). It is slower than the normal PDB plugin, so probably not suitable for large multi-frame files. Residues > 9999 are numbered from 0 rather than alphanumerically for compatibility with tleap.
Changing the default TER style
Two styles are supported for embedded TER cards. The format can be chosen at compile time by changing the following line in the source
#define DEFAULT_TER_STYLE TER_STYLE_xxx
Where xxx can be one of
TER_STYLE_LEAP: the TER record appears by itself, and does not have an individual ATOM id nor a residue ID. Although this style does not follow the PDB standard, is enough for the tleap suite of programs.
TER_STYLE_FULL: follow the PDB standard. Note that they take up one ATOM id, so large structures (e.g. with lots of solvent molecules) can run out of the limits imposed by some software.
Get the source
The patch can be obtained here.
Installation
Download the VMD sources. Go to the 'plugins' directory and apply the patch. Compile. Copy the .so file along with the others.
License
Questo/a opera รจ pubblicato sotto una Licenza Creative Commons.
Acknowledgments
Work partially supported by the VPH-NoE.
