Dear researchers
i am following the tutorial http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf
but in this tutorial its not mentioned how to restrain ligand in the pocket. I am using NAMD and VMD and want to find the binding energies of protein protein complexes. please give me some suggestions.
I am familiar with GROMACS and have performed protein ligand complex simutations and restrains etc. but i don't know how to do it in NAMD. please guide me.
thanks in advance
"User Defined Forces"
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node40.html
Thats not difficult, choose the molecule you would like to restrain, and mark in its occupancy (in pdb file) as mentioned in namd tutorial (http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix.pdf), you need to apply restraing force, that you need to take care of, then try running your md.
You can restrain by changing the pdb as Abhishek mentioned. The instructions are here: http://www.ks.uiuc.edu/Research/namd/2.9/ug/node27.html
All you need to do is decide which atoms you want to restrain and how tightly. However, if you want the protein to remain relatively fixed to the other protein then you'll want distance constrains which can be done with colvers: http://www.ks.uiuc.edu/Research/namd/2.9/ug/node55.html
A useful tutorial on making measurements is here: http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf
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