Dear all, I am interested in carrying out PCA analysis of protein and ligand complex in order to understand which ligand binds to protein and restricts the relative movement of the chains of receptor during simulation. I have carried out four simulations of 30 ns each - 1) with just the protein (receptor) in water 2) ligand A with receptor 3) ligand B with receptor and 4) ligand C with receptor.
If i am interested in comparing the effectiveness of ligand binding. Should I, use the NPT.pdb obtained from the 1st simulation as a reference to check the covariance of the backbone or Should it be the NPT.pdb obtained in the individual simulations? -- Regards, Prasanth. -- 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.
