[gmx-users] g_rms questions

[ChenYanjun]

Hi all,
   I learn to compare structures by g_rms.I have read the reference paper about g_rms.But I am not sure that I have grasped the idea completely.I have some questions as follows:
1)When I compare a pair of proteins,whhat are the objects to be compared.Are they all   atoms,c_alpha atoms or backbone .
2)Can g_rms be used to compare comformations of DNA or RNA molecules.
3)Are intrinsic difference between Rho and RhoSc? How to choose? Can they deal with peptides short as 5 residues.Is there some problems if I apply g_rms to compare peptides such as loops or secondary structures which are not quite globular.
   
　　　　　　　　ChenYanjun
　　　　　　　　chenyj at moon.ibp.ac.cn
　　　　　　　　　　2003-06-11