AmberTools-Analysis-Quick

In the last three years, I have used AmberTools to perform several molecular dynamics simulations of protein-ligand complexes. This repository is an attempt to provide easy to use script for the most common analysis I have performed in this period.

The scripts here are interactive and automated to allow the user more control over the inputs and outputs

For more information, see the AmberTools25 Manual

Special thanks to Dr. Oluyemi Wande and Dr. Adewumi Adeniyi for their guidance

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njikota-Traj:

combine your trajectories

A script to help you seamlessly combine your amber trajectory files

Usage:

#Clone repository
git clone https://github.com/SHEDOOMTC/AmberTools-Analysis-Quick.git
#copy njikota-Traj.sh from njikota-Traj/ into your working directory
# Make executable
chmod +x njikota-Traj.sh
#run
./njikota-Traj.sh

1. The script will request several input paramters interactively like your parm file, traj prefix, starting traj index, traj format, number of traj files, number of frames to process per traj, ions to strip, water residue name.

2. It assumes your traj files are named sequentially starting from 0 or 1 with a prefix and then an extension

3. You will have a stripped topology and stripped combined traj in NetCD format as the output

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rms-fluc-deviations:

Quickly analyze rmsd, rmsf, rog, globally and in the active site or specific regions

Usage:

#Clone repository
git clone https://github.com/SHEDOOMTC/AmberTools-Analysis-Quick.git
#copy rms-fluc-deviations.sh from rms-fluc-deviations/ into your working directory
# Make executable
chmod +x rms-fluc-deviations.sh
#run
./rms-fluc-deviations.sh

1. The script will first request input paramters interactively like your stripped parm and trajectory files, starting frame, ending frame.

2. Then you will choose one of "RMSD" "RMSF" or "ROG" analysis and also enter residue range (for active site or domain analysis) and atom masks

3. For any of "RMSD" or ROG" you choose, you will have to further select your reference structure (First frame, average structure or the minimized structure)

4. If you choose the minimized strucutre, you will be requested to enter a solvated topology and restart file of the minimization step (since the restart file is still solvated). This step is necessary to generate a stripped minimized structure to be used as reference

5. The names of the output files are hardcoded but usually reads "rmsd_minimized.dat" for rmsd using the minimized structure as reference

6. Any other detailed output needed will require the modification of the script

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Higher-fluctuations

Measure dynamic correlations between residue, and secondary structure changes

Usage:

#Clone repository
git clone https://github.com/SHEDOOMTC/AmberTools-Analysis-Quick.git
#copy corr-mat-sec-struct.sh from Higher-fluctuations/ into your working directory
# Make executable
chmod +x corr-mat-sec-struct.sh
#run
./corr-mat-sec-struct.sh

1. The script will first request input paramters interactively like your stripped parm and trajectory files, starting frame, ending frame, stride, residue and atom masks.

2. Then you will choose a basename to append to your output file

3. It will run correlation matrix and secondary structure changes one after the other

4. The output of the correlation matrix is in DAT format while secondary structure changes gives in AGR and GNU formats

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otu-dimension-cord-analys

Track your reaction cordinate such as distances, angles and torsions

Usage:

#Clone repository
git clone https://github.com/SHEDOOMTC/AmberTools-Analysis-Quick.git
#copy otu-dimension-cord-analys.sh from otu-dimension-cord-analys/ into your working directory
# Make executable
chmod +x otu-dimension-cord-analys.sh
#run
./otu-dimension-cord-analys.sh

1. The script will request several input paramters interactively like your parm file, traj file, start frame and end frame

2. It also request to choose one of distance, angle or torsion to compute

3. You can enter the masks you want to use (eg. 540@CA etc.)

4. You finally choose the name of the output file

5. This uses only atoms in its computation and cannot handle centre of mass calculations

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nweda-dimension-pca

Reduce dimension and extract the most important motions along n principal components (PCA)

Usage:

#Clone repository
git clone https://github.com/SHEDOOMTC/AmberTools-Analysis-Quick.git
#copy nweda-dimension-pca.sh from nweda-dimension-pca/ into your working directory
# Make executable
chmod +x nweda-dimension-pca.sh
#run
./nweda-dimension-pca.sh

1. The script will request several input paramters interactively like your parm file, traj file, start frame and end frame and name of the output file

2. It also request to choose the stride for performing the cutting step (for computational efficiency; choose between 100-500)

3. It will also request for the number of principal vectors to compute

4. It outputs two key .dat files for the principal components and their contributions

Note

The diagonalization of the matrix uses only the @CA atoms; if needed, you may have to edit the script

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strucuture-kachasi-mkpa

Collect the most representative structure in your system through clustering

Usage:

#Clone repository
git clone https://github.com/SHEDOOMTC/AmberTools-Analysis-Quick.git
#copy strucuture-kachasi-mkpa.sh from strucuture-kachasi-mkpa/ into your working directory
# Make executable
chmod +x strucuture-kachasi-mkpa.sh
#run
./strucuture-kachasi-mkpa.sh

1. The script will request several input paramters interactively like your parm file, traj file, start frame and end frame, and stride

2. It also request to choose the clustering method (hieragglo, kmeans, dbscan, average-linkage) and the number of cluster expected

3. You also enter the residue range (eg. 1-400) and the atom masks (eg. e.g., C,N,O,CA,CB)

4. Output files are hard coded to generate cluster number vs time, cluster population vs time, representative ad average strucutre of each cluster, and a summary file of clusters (number of frames, rmsd etc.)

Note:

This uses sieve of 10 internally and the script must be edited if there is need to change it.

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Ike-eji-aru-oru computation

Compute the fre energy surface of your system using the MMGBSA and MMPBSA protocols

Usage:

#Clone repository
git clone https://github.com/SHEDOOMTC/AmberTools-Analysis-Quick.git
#copy ike-eji-aru-oru.sh from ike-eji-aru-oru/ into your working directory
# Make executable
chmod +x ike-eji-aru-oru.sh
#run
./ike-eji-aru-oru.sh

1. The script will request several input paramters interactively like your parm file, traj file, start frame and end frame, and stride

2. Choose the stride to use only about 500-1000 frames for computational efficiency

3. Choose the ligand mask and residue list for energy decomposition

4. You will have to choose if it is GB (MMGBSA) or PB (MMPBSA) that you want to run

5. The igb for GB is hard-coded to 5 and saltcon to 0.15; for PB, the istrng is hard-coded to 0.100. Any needed changes will require editing the script

6. The output is a DAT file for the energy and decomposition results

Note:

To use more CPU, you can edit the script to impliment MPIRUN

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Kontakti-na-hydrogen-bondi-analysis

Analyze the most important contacts and hydrogen bonding in your systems between your active site residues and your ligand

Usage for kontakti analysis:

#Clone repository
git clone https://github.com/SHEDOOMTC/AmberTools-Analysis-Quick.git
#copy kontakti-analysis.sh from Kontakti-na-hydrogen-bondi-analysis/ into your working directory
# Make executable
chmod +x kontakti-analysis.sh
#run
./kontakti-analysis.sh

Usage for hydrogen-bondi-analysis:

#Clone repository
git clone https://github.com/SHEDOOMTC/AmberTools-Analysis-Quick.git
#copy hydrogen-bondi-analysis.sh from Kontakti-na-hydrogen-bondi-analysis/ into your working directory
# Make executable
chmod +x hydrogen-bondi-analysis.sh
#run
./hydrogen-bondi-analysis.sh

1. Both scripts will request several input paramters interactively like your parm file, traj file, mask for your active site residues and also for the ligand

2. It also request to choose the reference frame (either the first frame of the trajectory or the cordinate file of the minimized system)

3. You will have to choose the cutt-off distance for contact analysis, but the cut-off distance and angle for hbond analysis are hard-coded (3.5A and 135° respectively)

4. Contact analysis will generate total contact count, count by residues, native contacts and time series contact counts etc. (for more information, see the AmberTools25 Manual)

5. The hbond analysis runs in parallel and will generate outputs for when the residue or ligand is the donor (named res2lig and lig2res respectively). It will output hydrogen bond counts, occupancies and time series.

6. You can choose a base name to append to all the output file for ease of recognition.

Note:

This analysis uses all the available frames. If you need a section of your trajectory, you will need to edit the script

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