This is a simple script to truncate a protein/receptor structured based on a distance criterium with respect to the present ligand.
As a prerequisite, the scripts relies on AmberTools (cpptraj) to process the .pdb structure.
For the rest, the script is only reliant on commands, e.g. awk and sed, for text processing and manipulation which should be available in (most of the) Linux flavours
The script is simply run from the CLI:
$ bash TruncAndCap.sh
This should produce the truncated and capped complex. Please note that the caps will have missing heavy atoms. These are added automatically when loading the .pdb in leap to prepare your parameter and topology files.
The script is currently written in a (very) static way. In several places i added a MODIFY comment where you might want to change some things to work on your structures. Pay specific attention to file names and paths, the ligand residue number and the distance threshold you want to set.
Feel free to reach out if you have trouble running the script.
Everyone is welcomed to branch and/or enhance the script as they feel.
See modifications.txt for update history
Charles-Alexandre Mattelaer