[gmx-users] Suggestion on Umbrella sampling and peptide synthesis

rama david ramadavidgroup at gmail.com
Mon Oct 6 08:13:58 CEST 2014

Dear Friends,
     I want the suggestion from you on my plan of work. The plan is as
follow :

         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
latest version.?
      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,

 Rama David

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