[gmx-users] Suggestion on Simple protocol for MD..
ramadavidgroup at gmail.com
Wed Oct 1 11:53:39 CEST 2014
I want the suggestion from you on my plan of work. The plan is as
I have the protein pdb file in which two protein interact with
each other and the dimer
formed. The dimer is responsible for various bad effect in cell. So my aim
is to to inhibit the dimer formation. To do so, my plan is doing the MD
simulation of dimer for 50 ns or appropriate time to make stable
conformation. Then do umbrella pulling/sampling ( steered Molecular
dynamics ), so that I can find the residues that are most important in
interactions ( hot spot residues for interactions). Afterward design the
peptide from these hot spot to check biological activity.
My questions are as follows:
1. Is this approach is good or any other way to do this
2. I read about Computational alanine scanning, Is it possible in Gromacs
if it how to do it??
3. If any one do this work please send me the article link or article (
Surely I am also working hard to find and reading the article. I
have some good article too, but other good article also welcome. )
I am looking forward for great suggestions from you.
I am waiting eagerly.
I am very much thankful for your help and giving time for my problem.
With Best regards,
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