Scripts to share

Some home cooked scripts, mostly for VMD and Pymol

tcl scripts for VMD

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.

trick for residues with long residue names

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}