Jayaram@All these questions asked by you, are considered as some basic MD questions; it will not be helpful to address all of them once.

I highly recommend you to study some papers in this area.

Rome wasn’t built in a day.

I totally agree with Ramin Ekhteiari Salmas. There are many excellent review articles on molecular dynamics that you can easily find with a simple Google search. That's where I'd suggest you start to learn about things.

Good Luck

Dear Ramin and Anu

Thank you for the response.

I know nothing can be done in one day.

I am a microbiologist not a bioinformatician. .

I already did simulations for enzyme substrate complex. I am doing it successfully.

I need this simulation study very urgently for publication of my research paper. I have very less time.

I read many papers on simulations. So many things are not clear to me.

As you know simulation take so much of time. I cannot proceed with trial and error method for optimization of simulations based on my research objective. I just want to clear my doubts so that I can proceed for more accurate results as it is very urgent for me.

Because of that reason I asked this questions.

Anyway thank you for the suggestions and response

Regards

Jayaram C

If that's the case, see if the attached answers are helpful for you.

1. Is it possible to carryout MD simulations of best posed docked enzyme substrate complex?

Yes, it is possible

if so, what is the actual method to carryout MD simulations of best posed docked protein?

You have to extract the docked protein-ligand complex as one file.

or Do I need to do MD simulation and find out the ligand binding site and compare with that of docking results?

Not necessary as by performing docking, you are already defining the active site. But by performing the dynamics studies, you can come up with the stability of the ligand within the binding site.

2. To carryout MD Simulations of best posed enzyme substrate complex, which force field is more suitable?

There is no shortcut here; you need to dig in the literature. (study regarding the force field)

3. During periodic boundary settings, what shape of supercell/box is suitable for MD simulation of best posed docked enzyme substrate complex?

For providing periodic boundary conditions, we have choices to make for the selection of the box. You should select most general space-filling unit cell that comprises all possible shape filling space. Box may be bricked shaped volume for the efficiency and should be suited to study an approximate spherical macromolecule in the solvent. Example: Rhombic dodecahedron, smallest and most space filling unit cell. (Study regarding the unit cell)

4. While adding ions to the system, Is it sufficient to add the respective ions to neutralize the system or I have to add the ions according to the buffering concentration?

It is necessary to neutralize the system prior to simulations. For that it is necessary to add the counter ions according to the total charge of the system to better model most experimental or in vivo conditions. Moreover, buffer system create environment at a stable pH.

Read: http://www.sciencedirect.com/science/article/pii/S0006349598779974

5. If I have to neutralize the net positive charge of protein, Instead of chloride ions, is it possible to add acetate ions to the system?

Sure, you can add any ion (salt) to neutralize the system.

6. During equilibration, in the nvt.mpd and npt.mdp files the number of steps and time is mentioned as 50000 and 100ps. respectively. Are those conditions are ideal for the equilibration for MD simulation of best posed enzyme-substrate complex?

Not necessary.

7. For MD simulation of best posed enzyme substrate complex, what is the ideal time frame: 1ns or 5ns or 10ns?

There is no ideal time.

8. After MD simulation, how to find the amino acid residues involved in hydrogen bonding with ligand

Read: https://www.researchgate.net/post/How_do_I_perform_an_hydrogen_bond_analysis_in_Gromacs

9. How to use the results of MD simulations to carryout MMPBSA/MMGBSA to find the free binding energies of enzyme and substrate before and after binding?

You need to extract the pose obtained after performing the dynamics. I am not sure regarding the calculation of binding energies of enzymes and substrate before binding.

Dear Anu

Thank you for the great help. I will be grateful for that.

Your answers helps me a lot.

I have one more question please.

I am following the gromacs procedure for protein-ligand complex obtained from Bevan's lab. I am able to do simulation for enzyme-substrate complex. I have the docked enzyme substrate file also. if I use pdb2gmx command for a docked protein it is not creating the topology file because no force filed recognizes the ligand and showing the error. So then I have to create the topology files separately, then have to merge both, to proceed for the simulation. It is the simulation of enzyme substrate complex (protein-ligand complex). This procedure is not suitable for MD simulation of best pose docked enzyme substrate complex. If this is also the same procedure for MD simulation of best pose enzyme substrate complex, at what step I have to define the positioning of the substrate around best posed site in enzyme for MD simulation. Please help me with this. Thank you.

Thank you once again for the response.

I am little bit confused with the statement " This procedure is not suitable for MD simulation of best pose docked enzyme substrate complex". COuld you please elaborate, otherwise as far as I am understanding, you may get your answer in the section "Build the Complex" in the attached link below.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html

The method explained is for MD simulation of enzyme-substrate complex (i.e., protein-ligand) complex. I have created the complex as described in the method and I did simulations. But in the complex created the positioning of the substrate in the catalytic site is not defined. Here the Simulation is not done with enzyme-substrate complex where the substrate bound to catalytic site.

You have docked complex, right.

Yes I have docked complex. According to the procedure, we have to generate the topology files separately for enzyme and substrate, then we have to set complex system for simulation. Here we are not defining the positioning of the substrate in the best pose site. We are doing the simulation of enzyme-substrate complex but not doing the simulation of enzyme-substrate complex where the substrate is positioned in the best pose.

Sorry I am disturbing you

Still you can follow the same procedure for merging the two separate topology files and eventually you will find the answer regarding the stability of the protein-ligand complex after the simulations.

Yes, thank you very much for the response and suggestions. I will keep the updates

Good Luck!!