Dear researcher,
I want to generate a free energy landscape using Essential dynamics analysis. I calculated a free energy landscape using g_sham tool. But it is not giving the idea about the minimized structure.
So my question is
1- How to predict a least energy confirmation of protein for docking using MDS
2- I attach a figure and i want to generate this type of figure
please provide me a solution.
Thanks in advance.
You can use following tutorial. Its very good and simple:
http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html
After plotting your FEL in either ORIGIN or MATLAB etc. software, you can extract meaningful conformations corresponding to the minimum energy region from the text file or from software itself, and compare with the control system or the protein if you are doing protein-ligand study.
You can use following tutorial. Its very good and simple:
http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html
After plotting your FEL in either ORIGIN or MATLAB etc. software, you can extract meaningful conformations corresponding to the minimum energy region from the text file or from software itself, and compare with the control system or the protein if you are doing protein-ligand study.
Heartly thanks mam,
I will try if any problem then i will further ask to you.
If you got the .xpm file, then you can try the command below:
gmx xpm2ps -f file.xpm -o file.eps -do file.m2p -rainbow red (or blue)
which will render .eps file that can be viewed via Photoshop, tweak the levels and curves a bit and you will get a sharp image along with an energy bar. Rohit Shukla Daniel Madulu Shadrack
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