Dear all, I have carried out simulations of two homologous proteins (~38kDA) using Gromacs v4.5.3 using OPLS force field. The protein consists of three domains. Structural studies using cystallography reported earlier showed that the two proteins differ in the extent of orientations one domain can take with respect to other. However the reason for this difference is not clear from the structure as the size of the domain and region connecting them is almost the same in both. The only difference between the two are 32 residues spread over the sequence. Can anybody please suggest me as to how to go about with the MD analysis to find out the reason for this difference in the two structures ?
Visualization of the structures extracted from the trajectory showed the domain to be flexible in two proteins but to different extents. Thanking You, regards Anu -- 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.
