Why doesn VMD read the CONECT records from the PDB file?
VMD uses one of two ways to find which atoms are bonded. If both a PSF and PDB are given, then the bond records of the PSF are used. If a PSF is not given, then the bonds are determined from a distance search, but if the unbonded atoms are too close (this usually occurs with model building) they will be connected as well. The usual way to fix this is to include CONECT records in the PDB file. Since we don’t use this feature and have no programs that really need it, we don’t have anything in VMD to read those records. We realize that not everyone has X-PLOR so we’ve included a program which will convert the CONECT records to a PSF file. It is called ‘conect2psf’ and is located on our web site at http://www.ks.uiuc.edu/Development/MDTools/conect2psf/ . Only a binary for SGIs running IRIX 5.x is available.
