VMD-L Mailing List

From: William Howe (howew_at_mail.gvsu.edu)
Date: Mon Jul 20 2020 - 11:12:54 CDT

Hi, I'm new to TCL language, but have some experience with Python. I
am wondering what would the TCL script be to iterate over a directory
containing PDB files and create a binding pocket for each file
iterated over.

I know in VMD Graphical Representation I could use the atomselect
command 'protein and within 4 of resname LIG', and then save
coordinates to create a pdb file of the pocket but I would like to
automate this process for several dozen pdb files I am working with.

Say I have a Folder of PDB Files, here is the input and the desired
output(output name should be in the same format):
Receptor1.pdb --> Receptor1 Partial Pocket.pdb
Receptor2.pdb --> Receptor2 Partial Pocket.pdb
Receptor3.pdb --> Receptor3 Partial Pocket.pdb

Heres the directory I'm Working From:
C:\Users\Will\Desktop\School Junk\GABA Project\GABA Structures

Within this folder are several subfolders and each subfolder has
several other subfolders.

Sorry for the long post, this is my first one, any help is greatly appreciated.