Recently i am studying protein ligand interactions but i have problem in VMD how can I calculate number of hydrogen bonds, amino acids and distances through VMD
You can use Hbond command, and then count the number in the Hbond list.
For example, calculate number of backbone hydrogen bonds:
set D [atomselect $mol "protein and name N"]
set A [atomselect $mol "protein and name O"]
set lists [measure hbonds 3.5 30 $D $A]
set atoms [lindex $lists 0]
set Num [llength $atoms]
You can use the same method to calculate the contact number.
VMD can visualize the HBOND, but I don't think it can count them. Maybe you can write some tcl scripts to do this.
If your MD code don't contain the HBond tools, you can write a script. Python and bash is my suggestion.
Hi
If your ligand is small molecule then use ligplot and nucplot (hbplus) when protein/nucleic acid as ligand .
You can use Hbond command, and then count the number in the Hbond list.
For example, calculate number of backbone hydrogen bonds:
set D [atomselect $mol "protein and name N"]
set A [atomselect $mol "protein and name O"]
set lists [measure hbonds 3.5 30 $D $A]
set atoms [lindex $lists 0]
set Num [llength $atoms]
You can use the same method to calculate the contact number.
I prefer gromacs tools. However, if you want to calculate it in VMD, eg HB , you should go to Extensions> Analisys> HydrogenBonds. Here you select the file and make the selection of the two groups or molecules you want to evaluate, eg: Protein in selection 1 and ligand in selection 2 ( resname LIG or whatever you call it). Then you need to enable the option to calculate the hydrogen bridges and tick the window to write output files, in order to give you the detail among which atoms, HB occurs. Also you can change the angle and distance criteria, depending on how weak or strong the hydrogen bridge you are searching for ...
In the same direction, there are other tools in vmd, which let you calculate all that you mention. All this tools is detailed in VMD tutorials: http://www.ks.uiuc.edu/Research/vmd/current/docs.html#tutorials
Regards,
http://www.ks.uiuc.edu/Research/vmd/current/docs.html#tutorials
@Jingjing Guo
This method gives the number of H-Bonds only for one frame. For several or all frames, a loop should be used.
This is not so. You can evaluate all the frames at the same time, you must specify in the frames window: "all", or indicate the beginning and the end, with "b:e" format.
In fact, what is plotted is NºHB vs. frames ...
@M. Florencia
What I mentioned was about Jingjing's script.
Of course, the calculation in Hydrogen Bond window is for any frame we want!
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