From: Shehan Parmar (
Date: Sun Oct 22 2017 - 17:57:00 CDT

> Hello VMD-users,

> I have been working on a project that outputs a PDB file with atom
> positions and complete bonding information. I'd like to visualize this
> configuration with the appropriate bonds in VMD. I am aware that VMD
> doesn't read the CONECT information in the PDB. This led me to use PSF
> files along with the PDB to include proper bonding between atoms. I used "
>" perl file to convert the PDBs. However, when I use both the
> PDB and PSF files together, I am still seeing many incorrect bonds (i.e.
> oxygen-oxygen bonds in nitrate molecules). What could be causing this? Is
> there any way to edit the PSF for it to display the bonds correctly? Or is
> there a better way altogether for correctly diplaying a molecule starting
> with only a PDB? I have also considered using the psfgen tool, but based on
> its documentation, there doesn't seem to be a way to directly convert the
> PDB to a PSF file.



Shehan Parmar