Hi,
I performed 70ns MD simulation of protein system. Now I want to find hydrogen bond of specific atom of protein during the whole simulation. i want to know that specific atom makes interaction with which other atoms of amino acid as well as water molecules during my complete 70ns.
Please guide me in this regard.
Dear Sidra,
I guess that an utility to find H-Bonds is in most common visualization software, like VMD (see this http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/) or Pymol. Have you already checked them?
If you want to do it systematically: for each snapshot of the trajectory, record all possible hydrogen-bonding partners that are located within the threshold distance (e.g., = 135 degrees).
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*The list will include the potential hydrogen-bonding atoms of all water molecules and other small molecules, and the potential hydrogen-bonding atoms of the protein within a certain distance (decided depending on the dynamics of the region involving the atom of interest).
Hello Sidra
It's straight forward, you just specify the atom of interest as separate group in index file and then calculate the number of H-bonds over the production by gmx hbond option. this will give hbond.xvg file which you should open in excel to view the number of H-bond for each frame you have in your trajectory.
Good luck
Dear Veniero and Martin,
Thank you so much for your response. yup i've already checked the VMD but it's not useful in my case.
I have more than 5000 frames, it's not possible for me to find all the possible hydrogen partner manually.
i want to more elaborate my query, may you can understand what i mean.
i have 5700 number of frames of antigen-antibody complex system, i performed water box simulation using namd. Now i am looking for interaction of one nitrogen atom, that actually changed their partner in almost every frames, i want to know that how many partners they actually changed and which is the more consistent one in all. the partner can be the atom of other amino acids as well as water molecules.
Is there any way to plot graph or some thing like that.
Dear Amir,
I am using namd and gmx hbond option is working with gromacs files. I have files that showed how many atoms are involved in making interaction but which water atoms are involved i don't know. i'm looking for those all atoms. it give me in general that 167% water molecules are making interactions, but i want their number as well.
this is my plot.
i think there is an option in VMD to calculate hydrogen bonds over a trajectory.
i analysis section
I have another suggestion: download the "antechamber" package and compile it. You will find there a program called cpptraj which performs analyses on MD trajectories. Its native formats are the amber trajectories, but it can read also different file formats.
Then, with a bit of scripting, you should be able to implement the scheme suggested by Martin Klvana in his previous answer.
Probably you can do the same using a TCL script in vmd, which is also quite powerful.
Measuring distances and angles between atoms using their x, y, and z coordinates are simple mathematical operations; what might seem unfeasible at the first glance is the number of measurements that needs to be performed. This, however, is also very simple programatically using nested logical "for" loop operators: for every snapshot . . . for every pair of atoms in the list . . . measure distances and filter them by cut-off and store the data in a dictionary. Analyzing molecular dynamics simulations requires some scripting. There is no other way. Relying on build-in features in existing programs is just too limiting . . .
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https://www.python.org/
You can use PyMol, it is powerful enough and has friendly interface...
1. after the import of your pdb with 5000 frames, You can select the target residue/atom and expand the selection on 3-5 angs (atoms or residues). then make the inversion on the object and hide all around your residue and surrounding atoms/residues.
2. If You select your residue and find all polar bonds, all h-bond will be rendered.
If you performed MD in Gromacs You can use g_dist command and index.ndx file to make all steps from the first part and obtain smaller pdb...
Hi Alex,
i have a file in .dcd format. it is the output of namd. would you please tell me is there any way to open dcd file in pymol
Dear Sidra, this link https://sourceforge.net/p/pymol/mailman/message/31157939/ should be useful for You. If it doesn't, You can convert dcd to pdb with VMD visualizer.
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