[gmx-users] g_rms questions

David spoel at xray.bmc.uu.se
Wed Jun 11 07:56:01 CEST 2003

On Wed, 2003-06-11 at 03:09, ChenYanjun wrote:
> 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 .
you decide. C-alpha is common, all-atoms too.
> 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.
No idea what that means.

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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