Hello. May be angle cutoff should be pointed for H-D-A angle as in GROMACS but not for D-H-A angle? Because angle less then 20 degree for D-H-A angle is pointless for h-bond. Am I right? Thank you.
Thanks for the video @Mohamed shehata. Can you please help me on how can i find intra-molecular Hydrogen bond between 2 strands of Stem of RNA. I need to find particularly Watson-crick and Non-Watson Crick H-Bonds
Hello, thank you for your video. I computed the H bonds between chain a and chain b of my complex, for all the frames of the psf. I got the graph that from what I understood describes the number of h bonds during the simulation, and the document describing the h bonds. This document gives a list of H bonds, do you know what they refer to? to which frame in particular? is it the last one, or do you think is an average? Thanks, Camilla
Hiii, what I select for intermolecular hydrogen bonding between chain A and chain B. In my protein their is two chains ( 1 for antigen and 2 for antibody i. e. Heavy and light chain).
Hi, I've learnt a lot from your video. Thank you very much! However, I ran into a problem now and wonder if you could give me some kind suggestion. I performed MD simulation for a starch-water system by LAMMPS and obtained the trajectory file. When I conducted hydrogen bond analysis in VMD (version 1.9.4a53) for it, I always failed to see any hydrogen bond even if I have increase the D-A distance to 100 A and the angle cutoff to 120 degree. Because there is no protein in my system, I typed "all" in the selection 1 field. I have no idea what's going wrong. Could you help me with the problem?
Hi, Nice video I am working on battery cathode materials so when Li is adsorbed I would like to know how many Metal-Oxygen bonds are broken with time.. Can this be done with VMD too..Thank you!
Hello! An error window is displayed when I try to to run the H-bond research. I am using the windows version of NAMD 2.14 and VMD... Is it because this program run only on ubuntu? 😐
Hey, I am using the same method to get H-Bons for my water simulation. While visualizing through representation, I am easily able to see the H-Bonds. But, I am unable to plot it. I am also using psf and dcd files. Can you provide me any insight, where I am going wrong? Thanks! Cheers!
Hi, I have a question. I tried to find HBond by choosing selection 1 is "oxygen". Frame 0, I got HB around 27k bonds, but from frame 1 to the end, HB decreased so much, only around 700. However, if I separate every frame in every file, then it shows around 27k for every frame. Do you know the reason why? Thank you for your helping.
Thank you for the tutorial. One question: for comparing the number of HB among similar proteins, is it possible (and reliable) to calculate HBs using a single frame for each protein?
Besides the default angle part, I found another thing which is very confusing. When I used both HBonds Plugin and the "measure hbonds" command in terminal, I got different results even I used the same criteria.
@@Mohamedshehata Thanks for your reply. I just realized the difference is caused by the error on my codes for dealing the data, and had nothing to do with VMD. hhhhhh how embarrassing....
@@Mohamedshehata Is there a way to see which residues are involved in HB with the ligand along the trajectory OR only the total of HB as shown in the plots? And thanks for the video!
Hello. May be angle cutoff should be pointed for H-D-A angle as in GROMACS but not for D-H-A angle? Because angle less then 20 degree for D-H-A angle is pointless for h-bond. Am I right? Thank you.
Is there a way to also plot the (average) distance in A of the H-bonds along with this?
Thank you for your helpful tutorials.
What about H-bonds occupancy? Any trick or script for gromacs xtc trajectories?
this is really helpful, thank you very much!
Thanks for the video @Mohamed shehata. Can you please help me on how can i find intra-molecular Hydrogen bond between 2 strands of Stem of RNA. I need to find particularly Watson-crick and Non-Watson Crick H-Bonds
Hello, thank you for your video. I computed the H bonds between chain a and chain b of my complex, for all the frames of the psf. I got the graph that from what I understood describes the number of h bonds during the simulation, and the document describing the h bonds. This document gives a list of H bonds, do you know what they refer to? to which frame in particular? is it the last one, or do you think is an average?
Thanks,
Camilla
Hiii, what I select for intermolecular hydrogen bonding between chain A and chain B. In my protein their is two chains ( 1 for antigen and 2 for antibody i. e. Heavy and light chain).
Hi, I've learnt a lot from your video. Thank you very much! However, I ran into a problem now and wonder if you could give me some kind suggestion.
I performed MD simulation for a starch-water system by LAMMPS and obtained the trajectory file. When I conducted hydrogen bond analysis in VMD (version 1.9.4a53) for it, I always failed to see any hydrogen bond even if I have increase the D-A distance to 100 A and the angle cutoff to 120 degree. Because there is no protein in my system, I typed "all" in the selection 1 field.
I have no idea what's going wrong. Could you help me with the problem?
Hi, Nice video I am working on battery cathode materials so when Li is adsorbed I would like to know how many Metal-Oxygen bonds are broken with time.. Can this be done with VMD too..Thank you!
Hello!
An error window is displayed when I try to to run the H-bond research. I am using the windows version of NAMD 2.14 and VMD... Is it because this program run only on ubuntu? 😐
Sir , what is the purpose of measuring the hydrogen bond distances?
in the detailed file produced , what is the occupancy exactly and more importantly how to choose cut off for occupancy to select the best interaction?
Hey, I am using the same method to get H-Bons for my water simulation. While visualizing through representation, I am easily able to see the H-Bonds. But, I am unable to plot it. I am also using psf and dcd files. Can you provide me any insight, where I am going wrong? Thanks!
Cheers!
Hi how can we find the number of hydrogen bonds around the solute(spherical) particle with respect to distance(radial)?
Hi, I have a question. I tried to find HBond by choosing selection 1 is "oxygen". Frame 0, I got HB around 27k bonds, but from frame 1 to the end, HB decreased so much, only around 700. However, if I separate every frame in every file, then it shows around 27k for every frame. Do you know the reason why? Thank you for your helping.
I don't know, it depends on your system and your research question
Thanks for the video.
Do you know if i can use this VMD function for other groups of molecules than proteins?
sure you can
Thank you for the tutorial. One question: for comparing the number of HB among similar proteins, is it possible (and reliable) to calculate HBs using a single frame for each protein?
You would not be confident about your calculation.
Thanks for the video. Do you have a tcl script for doing Hbond analysis?
NO I tried the GUI but I am sure you can find in VMD script library
Besides the default angle part, I found another thing which is very confusing. When I used both HBonds Plugin and the "measure hbonds" command in terminal, I got different results even I used the same criteria.
did you use the same criteria of h-bond in the pulgin when you used "measure hbonds" command in terminal ?
@@Mohamedshehata Thanks for your reply. I just realized the difference is caused by the error on my codes for dealing the data, and had nothing to do with VMD. hhhhhh how embarrassing....
What about ligand
If you know the resname you can do the same
@@Mohamedshehata Is there a way to see which residues are involved in HB with the ligand along the trajectory OR only the total of HB as shown in the plots? And thanks for the video!