Thanks for the reply Babjan,

i have come out with the RMSD calculations already.

but the problem is with RMSF. i have a generated a data base of trajectories for the docked complex (in MOE). it has no option for RMSF analysis for the complexes.

As per your suggestion i'll try in Gromacs/NAMD

Thanks

Well, I have finished the MD using NAMD, I also got RMSD , but I don't know how to caculate the RMSF by NAMD. Could you tell me? Thank you.

Buen día, quisiera saber como calcular el RMSD atomo a atomo del

N-terminal Actin-binding Domain of Human Dystrophin y con la presencia de una mutacion puntual. Gracias

http://superpose.wishartlab.com/

https://zhanglab.ccmb.med.umich.edu/TM-align/ -> Gives RMSD and TMScore

Yao Yang Yang, For the calculation of RMSF you need to write a script. Then you can calculate the RMSF vs Residue graph.