[gmx-users] RMSD of Aminoacids

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 23 02:04:36 CEST 2009

Andy Torres wrote:
> Hi, I'm trying to compare two proteins with the same number of 
> aminoacids with g_confrms, and it works all right, but it gives me the 
> RMSD of the hole protein, and I need the distances (or deviations) of 
> each aminoacid. I know this data shoul be there, but I don't know how to 
> get it (I've got the mean structure of each protein, calculated with 
> g_rmsf, but this data is not fitted each other)

Have a look at g_confrms -h. Probably with the right index groups 
constructed you can fit with one group and observe the RMSD with another.


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