i want to plot total number of inter-molecular H_bond interactions between the drug compounds and target protein like below mentioned link.
http://www.nature.com/srep/2014/141110/srep06948/fig_tab/srep06948_F9.html
kindly guide me by using which software this plot can draw.
These are simple hydrogen bonding time series. The GROMACS gmx hbond (old versions call it g_hbond) is designed to do exactly this.
Above answers are useful. You can visualize the interaction via software 'Ligplot'. It provides hydrophobic interaction details too.
thanks for your meaningful suggestion Sabahuddin Ahmad . i used ligplot for visualizing interactions between the interface residues. but here i am here asking about how to plot the above mentioned graph of h_bond (attached link).
i implemented on Justin Lemkul reply. he understood what i am trying to ask.
Yes Sidra, Justin's Answer fits for your work... And that too, gromacs is free software. Discovery Studio might be not available, because of its commercial nature. I am not sure, whether you have Molecular dynamics data or something else, for which you are looking these suggestions. Please confirm.
The link, which you shared shows plot, which can be drawn via grace, origin etc. But for that you need data, which can be obtained by molecular dynamics simulation.
All the best.
Dear Justin Lemkul,
i used gromacs 4.6.5 for molecular dynamic simulation of antigen-antibody complex. i have downloaded gromacs 4.5.5 (old version) to plot the above mentioned h_bond graph. but now i have faced the version error problem.
old version of gromacs does not accept the new version .tpr file. is there any possible way to plot this graph with 4.6.5 version files.
Program g_hbond, VERSION 4.5.5
Source code file: tpxio.c, line: 2010
Fatal error:
reading tpx file (40ns.tpr) version 83 with version 73 program
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
No, .tpr files are not backwards compatible. Why use an old version? You should use a version that matches the one you used for the simulation.
Alright! the purpose of using the old version is to plot the same graph of h_bond that attached below (h_bond.jpg) and new version of gromacs doesn't make this sort of graph. i plot the h_bond graph using the version that matches my tpr file (attached below: ) but the old version plot attract me more and easy to understand.
This is the same thing. It's a time series of the number of hydrogen bonds. The image you're showing just has some fancy rendering with line colors and symbols, all of which is done very simply in XmGrace. But you have 50,000 data points in the time series, which is way more than what that image is showing, which makes your plot very crowded. So inherently it will look different. But the underlying data are the exact same concept.
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