Hi rajan I guess calculating radius of gyration for your whole protein with time will tell you about the size variation at difeerent time points or you canm say different frames. This is how you can cluster your whole trajectory PDBs into a few clusters and then get the representative PDBs from each cluster to finally select what you want.
Best Monica On Wed, Mar 5, 2014 at 8:42 PM, rajan kumar <rajugunju...@gmail.com> wrote: > Dear all, > > sorry for asking an off topic question. My protein is composed of two > domains connected by a flexible linker (15aa). after 50ns simulation i came > across the fact that one domain is flexible. so my question is that how > could i be able to calculate the size of molecule or radius of my molecule > and which conformation i should prefer to calculate the size of molecule. > your any suggestion will be very helpful. > thank you all in advance > > with best regards > -- > Rajan kumar choudhary > Senior Research Fellow > Department of Atomic Energy(Govt.Of India) > ACTREC TATA Memorial Center > Kharghar Navi-Mumbai > Mumbai-410210 > India >
