I assume when preparing the simulation box you put the ligand into the protein cavity, right?

Then it may also seem that the visualisation program shows the periodic image of the ligand, which actually sits in the protein cavity.

This often happens when the solute is not a single molecule by topology (i.e. the solute composes of more than one [ moleculetype ] ). When moving around the periodic boundary, it can happen that one part of the solute jumps across the boundary.

I suggest you to check the periodic box size and position (in VMD put to console "pbc box") and also to check program trjconv of gromacs distribution, to process your trajectory to look better.

Dear Sandeep, I am a bit puzzled with your snapshot.

From what I can see your ligand seems placed really far away from the receptor. Keep in mind that MD simulation are not intended for docking purposes.

I suggest you to prior dock the ligand with some docking software, afterward you can simulate the complex structure obtained from the the best pose.

I assume when preparing the simulation box you put the ligand into the protein cavity, right?

Then it may also seem that the visualisation program shows the periodic image of the ligand, which actually sits in the protein cavity.

This often happens when the solute is not a single molecule by topology (i.e. the solute composes of more than one [ moleculetype ] ). When moving around the periodic boundary, it can happen that one part of the solute jumps across the boundary.

I suggest you to check the periodic box size and position (in VMD put to console "pbc box") and also to check program trjconv of gromacs distribution, to process your trajectory to look better.

If you initially placed the ligand and protein unbound, then you can force them to aggregate during the MD using a biasing potential.

Check the recent approach: http://pubs.acs.org/doi/abs/10.1021/ci4006047

You may also wish to see what simulation times you would need to observe a binding event in an unbiased MD: http://pubs.acs.org/doi/abs/10.1021/ja202726y

if you are performing docking by MD, you may be interested in Metadynamics too: http://pubs.acs.org/doi/abs/10.1021/ja0512780

Another approach would be to use the obtained structure from docking as an input for replica exchange umbrella sampling (REUS) with principal component analysis. Okamoto Y. et al. DOI: 10.1002/jcc.21860 provided such a method for protein-ligand conformations which are comparable with experimental structures.

Thanks to all.. I did docking first to make protein-ligand complex, as suggested by Corrada and afterwards I am able to do its simulation.

Now I want to calculate binding energy calculation between protein and ligand after simulation. I read in some papers that g_lie can be used for that (first to do simulation of only ligand with solvent and then to do simulation of complex with solvent. finally using g_lie command to get binding energies.) But any tutorial on net is not clear about which commands to run to do it.

It is not a trivial question as many techniques exist. I think you need a bit of reading before you choose what you want to employ. For instance LIE and Jarzynski non-equilibrium give you the free energy estimate... Free energy perturbation or thermodynamic integration (TI) based methods are more accurate. Currently, REUS or metadynamics (PLUMED) would be more sophisticated to employ...but again it depends on your system. Do a bit of research before you start doing anything.

As Jan and Michael point out, once you are happy with your forcefield, you should use a biased free energy sampling method, such as umbrella sampling or umbrella integration or meta-dynamics. These are very powerful methods, and you should read up the basic theory before you use them (c.f. the Frenkel Smit book "Molecular Simulation" Scripts are already available on Gromacs, and via PLUMED which can be interfaced with Gromacs. It is also possible to use NAMD in the same way.

The basic idea is that you can impose an artificial force defined with respect to for example the distance between the centre of mass co-ordinates (COM) of the ligand, and (a) the protein respectively - or (b) a coordinates of the suspected binding site or (c) a distance and additional angles describing their relative orientation .

You can then correct for the bias mathematically (this is known as WHAM in the case of umbrella sampling), while in the case of well tempered meta-dynamics, there is a numerical specific factor. There are also other biased sampling approaches - all can be good. Of course if you have no water, you can just use simple docking approaches - but leaving out water may have dramatic (and imaginary/fictitious ) effects.

Best Regards,

Donal

 Dear Sandeep Singh sir, can i know what all steps you have followed after docking the protein-ligand complex by using some other software ?

Hello Shashidhar, after docking I chose the top pose of the ligand and obtained protein-ligand complex. Next, I performed the MD simulation of this complex. To perform MD simulation, I generated the topology and parameters of the ligand using swissparam (http://www.swissparam.ch/) and used gromacs software to perform MD simulation.

Dear Sandeep , you can use MMpbsa for binding energy calculation.its very handy .follow this link(http://rashmikumari.github.io/g_mmpbsa/).