Dear @Mahboobe this method is possible to calculate the free binding energy between two molecule after molecular dynamic simulation. In the case of docking, different force fields are used.
Thank you Alireza for your replies. When I am running the gmx mdrun command I have this warning: Some frames do not contain velocities. Ekin, tempratur and pressure are incorrect, the virial will be incorrect when constraints are present. How I can fix it? besides I do not know, where I should get the start frame and end frame for the last command? I would be grateful if you could help me to solve this two issues.
@@mahboobeazarakhsh1676 Please check the .mdp file. No I don't think you analysis would be wrong. You can bypass warnings with -maxwarn (e.g. -maxwarn 2)
Which type of energy should be calculated after last command for the protein-protein interaction? Lj-SR or Coul-SR or others? And how much should be the binding energy between two proteins?
For protein ligand interaction, as it was showed, I have chosen Protein-CY8,; CY8 referees to the ligand chain name. In your analysis please check the corresponding ligand (or second protein name). It could also be Protein-protein. Lj-SR or Coul-SR implicate short-range interactions like electrostatic. You can chose what type of interactions you are looking for.
Thank you for your great video.
Is it possible to calculate the binding energy between two proteins in a complex using this method?
Dear @Mahboobe this method is possible to calculate the free binding energy between two molecule after molecular dynamic simulation. In the case of docking, different force fields are used.
Thank you Alireza for your replies.
When I am running the gmx mdrun command I have this warning:
Some frames do not contain velocities.
Ekin, tempratur and pressure are incorrect, the virial will be incorrect when constraints are present.
How I can fix it?
besides I do not know, where I should get the start frame and end frame for the last command?
I would be grateful if you could help me to solve this two issues.
Dear Mahboobe, check the nstfout and nstvout values in the .mdp file. They should not be zero. You also need .trr file containing velocities.
Thanks, How much should be nstfout and nstvout? With this warning my results for the energy is incorrect?
@@mahboobeazarakhsh1676 Please check the .mdp file. No I don't think you analysis would be wrong. You can bypass warnings with -maxwarn (e.g. -maxwarn 2)
Which type of energy should be calculated after last command for the protein-protein interaction? Lj-SR or Coul-SR or others? And how much should be the binding energy between two proteins?
For protein ligand interaction, as it was showed, I have chosen Protein-CY8,; CY8 referees to the ligand chain name. In your analysis please check the corresponding ligand (or second protein name). It could also be Protein-protein. Lj-SR or Coul-SR implicate short-range interactions like electrostatic. You can chose what type of interactions you are looking for.
Could you say please what's the name of this method for calculating binding energy? I mean how it is refered in articles?
If you are doing this analysis it is in KJ/mol, other applications like Autodock reports as Kcal/mol
how to calculate interaction energy using desmond maestro
I haven't work with Schrodinger maestro. But I will look into it.