Dear Rajan,
Since you raised your question about calculating the radius of your molecule.
here my suggestion, a bit long back I heard about the program HYDROPRO
I am not sure its going to be work for you, but you may give a try.
I think the program calculates the radius of gyration !
best wishes,
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 e
Dear Rajan kumar choudhary,
could you explain why you expect the volume to depend on the conformation of the
molecule? Do you have some effective volume in mind, e.g. the elution volume
during size exclusion chromatography?
Regards,
Tim
On Wed, Mar 05, 2014 at 08:42:21PM +0530, rajan kumar 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 mole
