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https://github.com/bradenkeiser/amber_protocol

Complete automated HPC protocols for running complexed MD simulations in Amber and subsequent PBSA and per-residue decomposition analysis using a model HMG-CoA reductase dual-ligand system, uses Bash, Python, and R
https://github.com/bradenkeiser/amber_protocol

amber automation bash complex decomposition hpc md protocol python r simulation

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Complete automated HPC protocols for running complexed MD simulations in Amber and subsequent PBSA and per-residue decomposition analysis using a model HMG-CoA reductase dual-ligand system, uses Bash, Python, and R

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# Amber Protocol for Complexed Protein Simulation and PBSA Evaluation 




# General information for running Amber Protocol



This repository is for running a complexed simulation of a protein and its ligand. It uses the HMG-CoA Reductase docked with NAP and HMG as a reference example. There are three PDF files associated with protocols for running simulation and PBSA, accordingly: 



1. Part1_HMG-Simulation-Protocol.pdf --> This is a lengthy review of using the qm_protocol directory for running a complexed MD Simulation

2. Part2_PBSA-protocol.pdf --> This is the protocol for performing a PBSA examination within Amber following simulation

3. Part3_Decomposition-Cleaner.pdf --> This is a way to generate a more easily digested decomposition file while running the PBSA calculation. It is paired with an R script for generating a nice box plot of the data.



The PDF instructions relate to running amber through job submission on a TARA HPC server. A plethora of files are available and utilized largely from a core 'qm_protocols' directory. These scripts encompass running parameterization of the complexed system, NVT and NPT equilibration, and production runs. In addition, there are a variety of scripts for running standard RMSD/RMSF analyses through python and/or R. Finally, there are methods for running a PBSA analysis using the MMPBSA.py program within Amber. 



**For an example: **



Examining pt1_input-parameterization_2024.sh will reveal the methodology employed to parameterize the initial system using an optimized PDB file of the complexed structure. It will run through the complex, the solitary protein, and the solitary ligand files to craft amber-ready inputs for subsequent steps. This method would usually automate the use of Gaussian to acquire various RESP charges of the ligands; however, I have supplied these within the  directory of , and they are auatomatically drawn into the generated and nested  directory for the run. 



# Running PBSA and Decomposition Evaluation



PBSA and a subsequent per-residue decomposition color-coded bar chart can be generated by following their respective PDF protocols in the main directory here. These protocols run through an automated setup for a complexed system and will generate a custom-denoted PBSA analysis based on start and end frames. The scripts assume a 5ns PBSA run, taken from the last 5ns of the simulated production run. 






# Notes Regarding Dependencies

These scripts require a large number of dependencies that were curated on the job submission server. While these protocols work 'out-of-the-box' on that system, they will likely need a series of tweaks in order to effectively run on non-specific HPCs or local environments. Nonetheless, I hope these serve as a strong springboard for those who may be struggling to fine-tune simulation runs and analysis strategies of complexed systems.