Very good and easy gromacs process explained in 2 sessions, thanks, how to visualize these output files in VMD, plz do a video on protein-ligand gromacs simulation, because gmx tutorial on prot-lig is complicated
Thank you Dr. For your wonderful help. I have a question. If I want to do this for a ligand~protein complex generated from Autodock vina. How parameters should change?
I recently docked a small molecule to a protein.pdb and docking resulted in -7 kcal/mol. Do you have a GROMACS tutorial for MD simulation to assess potential effectiveness of a potential drug inhibitor?
Thank you for the tutorial. I have a question about the RMSF analysis of protein & ligand complex of an MD simulation. Is it possible to analyze and compare the RMSF result of a protein and its complex with a ligand?
Dear sir, your video was very helpful to me. Plz can you recommend any GPU that supports intel graphics because there is no nvidia graphics in my system.
Please clear me the step that after installing cmake and how can get protein chains? Because my protein not showing data like your protein as "single" chain etc????
Sir could you please post the command for Hydrogen bonding , SASA, secondary structure and radius of gyration please sir it would be really helpful for me
Thanks for the video. Would you please make a video on protein-protein complex MD simulation on grimaces? How can I introduce GROMACS which is my ligand protein and which is receptor protein I am very much confused about that.
First of all u have to do molecular docking using protein-protein docking tools, and have to use the complex to perform MD simulation. Gromacs doesn't recognize weather its a ligand or receptor, you can use similar approach as i did in above tutorial for your complex. After completion of MD, u can do additional analysis such as H-bond, ionic bond interaction etc., with ur complex. remember if your ligand is not a protein molecule, the tutorial is completely different
Very good and easy gromacs process explained in 2 sessions, thanks, how to visualize these output files in VMD, plz do a video on protein-ligand gromacs simulation, because gmx tutorial on prot-lig is complicated
Thank you Dr. For your wonderful help.
I have a question. If I want to do this for a ligand~protein complex generated from Autodock vina.
How parameters should change?
Sir gmx grompp -f ions. Mdp -c water_box.gro -p 1.top -o ions.tpr command is not run in my computer
Where did the ions file come from? I did not see this as an input in any of the preceding code
ions.mdp is in the description above
I recently docked a small molecule to a protein.pdb and docking resulted in -7 kcal/mol. Do you have a GROMACS tutorial for MD simulation to assess potential effectiveness of a potential drug inhibitor?
Thank you for the video. Is it possible to create a trimer from a monomer on Gromacs?
Sir ,how much time it takes to complete mdrun?
sir .. thanks for your explication.
how to find the potential energy or the total energy for the protein only.
Sir how to use g_mmpbsa in gromacs?
Thank you for the tutorial. I have a question about the RMSF analysis of protein & ligand complex of an MD simulation. Is it possible to analyze and compare the RMSF result of a protein and its complex with a ligand?
Thanks for the explanation
I have a question, How could u get the ions.mdp file?
Very nice explanatory Videos Sir I have a doubt how to use MD Simulations in loop modelling in protein pls explain ..
Thank you for your comprehensive video, Can I use Gromacs to simulate a hybrid molecule containing monosaccharides and amino acids together?
Yes you can!
@@jaannawaz2007 Can you suggest me how to generate pdb file for my new molecule ?
Dear sir, your video was very helpful to me. Plz can you recommend any GPU that supports intel graphics because there is no nvidia graphics in my system.
Please clear me the step that after installing cmake and how can get protein chains? Because my protein not showing data like your protein as "single" chain etc????
Last step of making graph ...I don't understand how to create graph of rmsd
Sir could you please post the command for Hydrogen bonding , SASA, secondary structure and radius of gyration please sir it would be really helpful for me
Ions, Md files are not generated in my folder, can you please help me with this.
could you please tell me how this full_md1.txc file generated? is it automatically generated??
Thanks for the video. Would you please make a video on protein-protein complex MD simulation on grimaces? How can I introduce GROMACS which is my ligand protein and which is receptor protein I am very much confused about that.
First of all u have to do molecular docking using protein-protein docking tools, and have to use the complex to perform MD simulation. Gromacs doesn't recognize weather its a ligand or receptor, you can use similar approach as i did in above tutorial for your complex. After completion of MD, u can do additional analysis such as H-bond, ionic bond interaction etc., with ur complex.
remember if your ligand is not a protein molecule, the tutorial is completely different
@@jaannawaz2007 Thanks a lot. I will try. If you can please make a video on it. You are really helpful.
nice :-)
Thanks 😀
How to retrieve the PDB after MDS for molecular docking
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