[gmx-users] g_rms questions

[David]

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.
yes.
> 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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