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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.