Thank you karis
The Lysozyme in water tutorial is suitable for protein simulation ?
Yes, the steps can be used for simulating any molecule as long as the forcefield has the topology information for it (which is true for most proteins and nucleic acids molecules). If you run into any issues where the forcefield doesnât have the residues you need defined, you can refer to the fifth tutorial on protein-ligand simulations.
If I complete Lysozyme in water tutorial and the results in taking protein RMSD is comparable with protein_ligand RMSD (protein_ligand tutorial) to know the stability of drug in protein is possible?
A low and stable RMSD tells you that the molecule doesnât change that much from its starting structure, so just the RMSD of the protein_ligand should tell you if itâs stable, comparing it to RMSD from a simulation of the protein alone is only necessary if you want to know if the ligand makes it more or less stable.
Thankyou Karis
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As I understood you want to compare the protein-ligand complexes to find a better ligand which binds to the protein and stays in a stable configuration. Am I right?
First, how you put the ligand in a binding site of the protein would be critical.
My recommended way is to use molecular docking to get the protein-ligand complexes. you can dock five ligands with the protein using appropriate molecular docking software.
Then you can get the docked ligand configurations (usually in sdf or mol2 format). You can convert the sdf or mol2 (or other) coordinate files of the ligands to PDB format and then put the coordinates of the ligands in pdb format at the last of the protein pdb file, separately for each ligand. These are five systems you are going to do MD.
After the MD simulations, you can get the trajectory and the final structure. Then you can do the analysis.
RMSD would be helpful. However other analysis would also be critical and useful. Also, the way you are doing RMSD calculation would be critical. I am saying about the groups you are using for âleast square fitâ and âRMSD calculationâ.
Also you can use VMD to visually look the trajectory as a movie. Then you can decide which molecules are stable and whether the results of other analyses agree with the things you can see visually.
When I had done this kind of thing, I calculated the RMSD of the ligands and complexes, least square fitting the complex both times. The results agreed with the things I saw visually.
You can try other analyses like gmx distance, gmx sasa, gmx gyrate, gmx rmsf .
Thank you Dulaj