Tutorial for Protein-ligand complex MD simulation
Kindly provide a tutorial for protein-ligand complex MD simulation in SAMSON.
Also provide guidelines to save and analyze the MD trajectories for data analysis and interpretation (such as RMSD, RMSF, PCA, etc.).
Also, kindly tell me is it possible to simulate the protein-membrane complex in SAMSON? If yes, how?
Dear @sudhir ,
For the protein-ligand simulation, you can check out the Ligand Path Finder tutorial for Ligand Path Finder Element. You can also check out the Ligand unbinding pathway search tutorial for the free Ligand Unbinding Search Element (available only on SAMSON 0.7.0).
As for saving MD trajectories, you can check out the tutorial on exporting atoms trajectories along paths which uses the Export Along Paths Element. This Element allows you to export trajectories into PDB files which you can further analyze using other software.
You can also do some analysis and post-processing in SAMSON thanks to the Python Scripting Element, you can check out the Python Scripting guide for more information, for example, the Computing RMSD sample.
To simulate a protein-membrane complex you can use the GROMACS Wizard Element, using this Element you can easily prepare your system for GROMACS simulation, minimize and equilibrate the structure, and simulate your system using GROMACS. See the GROMACS Wizard tutorial for more information.
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