Dear users, Which analysis do you suggest to examine the effect of ligand on protein?
1.)For quality assurance: RMSD,RMSF and Radius of gyration for free and complex form 2.)For structural analysis: ISA (interface surface area), the number of hydrogen bonds between protein and ligand, secondary structure for free and complex form 3.)Principial component analysis: The eigenvalues versus the first 30, 40 or 50 eigenvectors Projection of trajectory onto onto the first five or ten eigenvectors Projection of trajectory onto the plane of first two eigenvectors Cosine Content of some eigenvectors Are these analyzes adequate? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
