This repository stores useful sample codes I used in Ray Luo lab at UCI. Assisted Model Building with Energy Refinement (AMBER) software package is used in our lab for molecular dynamics simulation.
- 1MD_prep: Scripts for MD input files preparation. Package required: tleap
- 2Minimization: Scripts for free energy minimization before MD.
- 3MD: Scripts for MD (Heating + NPT ensemble + NVT ensemble).
- 4RMSD: Input files for trajectory RMSD calculation. Package required: cpptraj
- 5MMPBSA_prep: Scripts for MMPBSA input files preparation. Package required: tleap, cpptraj
- 6MMPBSA: Scripts for MMPBSA calculation.
- 7Native_Contacts: Scripts for calculating the fraction of frames for each contacting atom pairs with reference to the first frame. Package required: cpptraj
- 8Analysis_prep: Scripts for preparing stability score of each trajectory, RMSD images, MMPBSA images, MMPBSA data points sample.
- 9Score_Analysis: Based on the stability scores, analysing the most probable candidate of binding poses for different ligands.
- 10MMPBSA_Analysis: Based on the sampled MMPBSA data points, testing hypotheses using t-test.
- 11Visualization: Scripts for easier MD trajectory visualization. Software required: VMD, chimera