Dear all, I am working with a protein having phosphorylated serine and threonine residues. I will be performing ligand-protein MD. These phosphorylated amino acid residues are not located in the active site of protein. Should I just replace the phosphorylated serine and threonine residues with serine and threonine before MD preparations? Or shoild I ignore them because they will not be involved in any interactions with the ligand? Or do we have different force fields for the phosphorylated residues ?
Your suggestions are highly appreciated. Thank you. Sincerely, Mr. Swapnil Bhujbal PhD Scholar, School of Medicine, Chosun University, South Korea. -- 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.
