Hi everyone, I need to run some MD simulations with a protein where a particular serine should be phosphorylated. Since in the original pdb the serine is actually not, I guess I should modify something 'by hand'. I'm going to use AMBER-ILDN ff. Can anyone of you tell me what should I do? My first guess was to generate the topology and then directly substitute my serine with the phosphorylated one (looking for the AMBER-ILDN parameters), but sincerely I don't know if this is the correct way to proceed.
Thanks a lot for your support! Simone -- 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.
