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jaimergp / prep-mcpb

Prepare a metal-containing structure for parameterization with MCPB.py using UCSF Chimera and AmberTools
MIT License
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prep-mcpb.py

A step 0 for your MCPB.py protocols!

This script uses UCSF Chimera and AmberTools to preprocess a metal-containing structure for MCPB.py parameterization by following the recommendations found in Amber's MCPB.py #20 and Heme tutorials.

Installation

The script itself does not need installation, but it does require some stuff to be installed in your machine:

UCSF Chimera must be downloaded and installed manually. Everything else can be installed in a new conda environment with:

conda create -n mcpb -c insilichem -c AmberMD pychimera ambertools=18 scipy
conda activate mcpb

It has only been tested in Linux (Ubuntu 18.04).

Examples

Right now, I have checked it against PDB IDs 1OKL and 4ZF6. In other words, download a copy and run:

# Structure from tutorial 20
python prep-mcpb.py pdb:1OKL
# Structure from tutorial 20 (heme)
python prep-mcpb.py pdb:4ZF6

Disclaimer and help

This is a very rough attempt at familiarizing myself with the MCPB.py toolset. The main idea is to create a UCSF Chimera GUI extension to guide all the steps, but I will only do that after getting the basic workflow right. Please submit an issue if you test it and find errors in any structure (attach the files if possible), or if you feel that the current approach does not fit your workflow.