I performed MD simulation of ligand-protein complex in Gromacs and now I would like to visualize the h-bonds formed between ligand-protein over the course of MD simulation. I tried to set surrounding residues as 5 angstrom of ligand and representation coloring method - Type, Drawing method - HBonds. But it did not work out. It only shows H-bonds within protein.
Looking help from VMD expert.
Use hbond command to see the hydrogen bonds over the simulation time scale. I'll suggest use ligplot or discovery Studio 2D map for visualizing the hbond interactions.
If you only want to use vmd. Then you can use hbonds plugin of vmd.
Thanks for your answer, but I would like to visualize it in VMD for each frame in 3D. Whatever, you mention that deals with 2D h-bonds.
I've not used vmd for that. But pymol, discovery and schodinger is very useful for that and very easy.
There is an options of visualizing hbonds in "graphical representation" section. There you can also choose the particular residues.
I would show the residues within 3 A from the protein (same residues as within 3 of resname LIG) and then press 2, then click both ligand and protein parts corresponding to the H-bond
Dear Eko, thanks for your answer but it seems your approach works well with the constant H-bond forming atoms of lig-protein in a trajectory. I would like to calculate h-bonds of lig-protein from a trajectory where H-bonds forming atoms change time to time as simulation proceed. when I select 4 angstrom residue with the keywords you given and use draw style, coloring method - type and drawing method - HBonds, it show H-bonds within solvent-protein, protein-protein but not with the lig-protein. I hope you understand what I mean. Looking forward.
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