Can anyone please help me on how to choose hydrogens for calculating H-Bond distance in a particular protein… When I am visualizing my protein in pymol, unable to figure out, which hydrogens are interacting with each other… Please help me on how to choose hydrogens and make index file so that I can calculate distance between then using gmx distance command
Gromacs automatically classifies atoms according to which are hydrogen bond donors and acceptors. You can read it here: gmx hbond — GROMACS 2019 documentation " OH and NH groups are regarded as donors, O is an acceptor always, N is an acceptor by default, but this can be switched using -nitacc ." You can check the distance by using -dist option. for example gmx hbond -f name_of_xtc_trajectory_file.xtc -s name_of_tpr_file.tpr -dist hbond_distance.xvg
If you want to check the distance between specific groups, you need to create an index file in advance, check here how to do it gmx make_ndx — GROMACS 2019 documentation or here you have an example KALP-15 in DPPC and you add index file in gmx hbond command: gmx hbond -f name_of_xtc_trajectory_file.xtc -s name_of_tpr_file.tpr -n your_index_file.ndx -dist hbond_distance.xvg
I don’t know is it possible in Pymol to show where hydrogen bonds are. You can check the distance and angle. Here is Hydrogen bonds — GROMACS 2021.4 documentation hydrogen bond criteria, I use mostly default distance between acceptor (A) and Donor (D) is 0.35 nm or lower and H-D-A angle 35 degree or lower
Thank you sooo much for explaining… I will try to apply it…
Can you please help me on how to plot graph between H-bond distance and number of frames. Just like the one I am attaching here:
You can calculate the distance between any pair of atoms (or any groups of atoms) with gmx distance.
okk sir… i will try to do it…