Hello,
I need to check which water molecules (MD simulations) with their specific water IDs are coming at the catalytic pocket of my protein within hydrogen bond distance in 500 frames, i.e., in each frame which water ID is making Hbond with the residues.
I have tried using Hydrogen Bond plugin tool of VMD, however, it only gives me the general name Water-O and no particular water ID like, TIP39116
If I start checking every frame manually then it becomes a tedious job. So, I am eagerly looking for a TCL script or any specific program by which I can identify the specific water ID of all frames.
To be more specific regarding my problem, I am hereby attaching the hbond.dat and hbond-details.dat output files from Hydrogen Bond plugin tool of VMD.
I am eagerly waiting for your kind help and suggestions.
Thank you for your consideration.
Hi,
find attached a quick solution for your problem. The script calculates all hydrogen bonds between a donor and an acceptor selection, returns the water oxygen atoms, and selects the full residue afterward. Currently, the selections are hardcoded and but you can simply extend the script to your needs. If you need the resid or resname, update line 31.
Hello Lukas Schulig Thank you for your solution. It really helped me a lot.
Apart from modifying the script at line 31, I have also added a column that shows frame number.
However, one issue arising from this script is that it returns all the water molecules that make hbond with either one or more residues, depending upon the selection of acceptor atom is more than one residue. For example, in my case I have the acceptor selection- name N and resid 143 144 145, and donor selection- water. The output it is giving me is this 6746 1856 7068. Here, only the water ID 7068 makes hbond with N atom of all three residues. Whereas, water IDs 6746 and 1856 makes hbond with N atom of 145 and 143, respectively.
I only need those water molecules that make hbond with all the residues mentioned in the selection and not with one residue, i.e. water Id 7068.
Therefore, are there any changes that I must make in the script to get this kind of result?
I have attached the modified script for your kind consideration where I have made changes in line 31 and 33.
I will look forward to your reply.
Thank you
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