Some home cooked scripts, mostly for VMD and Pymol
vmd -dispdev text -e <script-name>.tcl
molecule.tcl TCL script for VMD to test the structure and/or topology of a small molecule. It generates pdb and psf files, and by loading them into VMD, you can spot the most common errors: missing and mislabeled atoms. If your initial pdb file has a residue or atom names, not mentioned in the topology file , the script would not produce output.
sasa-residue.tcl TCL script for VMD to print out SASA value for each residue of a structure. Edit to provide the pdb file name, prefix if you wish, and total number of residues.
Resnames more than 3 letters, like carbohydrates (sugars), small molecules (CGenFF) etc in the script for psfgen add:
segment SEG {
first none
last none
pdbalias residue RES RESNAME
pdb molecule.pdb}