Hi,
I'm new at MD. so I want to know more about protein preparation steps.
I wanna work with gromos54a3
and
is it important to edit orientation of these residues CYS, GLN, ASN? WHY?
and
is it important to edit protonation state of these residues CYS, LYS, GLN, ASP, HIS? WHY?
Here is the latest gromacs documentation file: https://manual.gromacs.org/documentation/current/user-guide/index.html
To prepare a protein for Gromacs Molecular Dynamics (MD) simulation, follow these steps: obtain the protein structure, remove water and ligands, check for missing atoms, and structural issues, assign chain identifiers, and check for unresolved residues. Select the appropriate force field, such as Gromacs54a3, and add missing hydrogens. Using the steepest descent and conjugate gradient algorithms, perform energy minimization to relax the protein structure. Solve the system using an appropriate solvent model, add water molecules, and perform ionization and neutralization if necessary. Generate topology files using tools like GROMACS pdb2gmx and editconf. Set up parameters for the MD simulation, including the integrator, time step, temperature, and pressure coupling, and run the simulation using Gromacs tools. Analyze the trajectory data to obtain insights into the protein's behavior. Careful preparation and parameterization are crucial for obtaining meaningful results in MD simulations.
"Is it important to edit orientation of these residues CYS, GLN, ASN? WHY?"
Yes, it is important to create the starting structure with reasonable accuracy so that you can get good results. The orientation of these can influence the local geometry that can ultimately affect the overall dynamics of proteins.
"Is it important to edit protonation state of these residues CYS, LYS, GLN, ASP, HIS? WHY?"
Yes, if you want to model the natural state, then you have to create properly protonated residues. The protonation state will dictate the side-chain h-bonding propensity that will cause the altered conformational and energetics basins that may or may not truly reflects the underlaying system.
You should "REDUCE" program that can handle most of these automatically. Moreover, gmx pdb2gmx is also reasonably good at guess the protonation states, but it is advised to use Reduce.
1. I want to know more about protein preparation steps.
You can check the gromacs manual as mentioned by Susanta Roy or alternatively, you can check the manual by Justin. (GROMACS Tutorials (mdtutorials.com).
2. is it important to edit orientation of these residues CYS, GLN, ASN? WHY?
Yes, you can check the score by using ERRAT, Verify3D and ramachandran plot
3. It is important to edit the protonation state of these residues CYS, LYS, GLN, ASP, HIS? WHY
Yes, if you have identified that the default protonation state of your protein not mimic the natural state as mentioned by Ayaz Anwar . So it is the best if you can check with literature, check protein pocket residues (5 Å from ligand) and compare with protonation generated by pdb2gmx tools.
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