VMD is a popular molecular modeling program. VMD is a powerful software for trajectory analysis. #modeling #dynamics #molecular #simulation #trajectory
how did you even create .xtc file which has a lot of frames? I am having issues with making multiple frames for movie making. A lot of videos show just load .xtc file but nobody even mentioned how to create .xtc file where you can have tons of frame
one click is missing when you showed the beads over 0:501 frames.. i tried in my case no such beads spread over binding pocket site?... what did i missed however i followed your steps? secondly i want to ask that how to make h.bond graph between ligand and particular residue. for example TYR81 and rename unk? can you explain in detail. and thank you this video was of great help.
Are you talking about Receptor-ligand complex? If receptor is a protein then you can calculate C-alpha or backbone RMSD. RMSD of ligand will consider all heavy atoms.
@@dianaa.valencia3910 I think if you split the frames after getting the extreme frames (eg 30 or 90) into pymol and individually show them as surface, that will work.
Thank you so much. highly recommended
Moore Matthew Walker David Thompson Amy
How to save the movie
how did you even create .xtc file which has a lot of frames? I am having issues with making multiple frames for movie making. A lot of videos show just load .xtc file but nobody even mentioned how to create .xtc file where you can have tons of frame
You will get .xtc trajectory after running MD simulation. GROMACS produces two types of trajectory files (.xtc and .trr).
one click is missing when you showed the beads over 0:501 frames.. i tried in my case no such beads spread over binding pocket site?... what did i missed however i followed your steps?
secondly i want to ask that how to make h.bond graph between ligand and particular residue. for example TYR81 and rename unk? can you explain in detail.
and thank you this video was of great help.
Do you know a way to calculate the RMSD of the complex?
Are you talking about Receptor-ligand complex? If receptor is a protein then you can calculate C-alpha or backbone RMSD. RMSD of ligand will consider all heavy atoms.
how you have created npt.gro file?
I downloaded VMD after trying for several hours and im not even able to see the main file window.... this is so sad
Can you pls explain how to perform principal component analysis?
I will upload a video on PCA.
Have you ever handle the error where the full structure is not shown? I'm getting error message while trying to display surf visualization
@@dianaa.valencia3910 I think if you split the frames after getting the extreme frames (eg 30 or 90) into pymol and individually show them as surface, that will work.
How to create npt. gro file?
Using GROMACS gmx grompp command..