From: Windle,Stephen (
Date: Tue Oct 31 2017 - 15:52:54 CDT

VMD Users,

Good afternoon. I am very new to the VMD software, and I am working on putting together a script for a specific purpose, but I am unsure how much of it can be done as a single script. Essentially, I want to measure the distances between all the side chains of a specific amino acid in a given protein (for example distances between all the valine side chains). However, I want to be able to load anywhere from 1000-10,000 molecules into VMD and have the script do this for each molecule consecutively, exporting them into individual files (I should be able to write a loop for this, I imagine). So far I'm able to load a molecule and isolate the side chains of a specific amino acid. So my two key questions are this: Can a loop be written to load every .pdb file in a given folder, and what are the console commands to measure the distance between each side chain once they've been isolated into a named selection. I have tried searching through the indexed messages but to no avail. If someone could point me in the right direction that would be greatly appreciated. Thank you!


Steve Windle