[gmx-users] rmsd on homologous protein structure

[Mark Abraham]

Tatsiana Kirys wrote:
> Hi,
> 
> i want to calculate rmsd on homologous protein structures that have different residue numbers. 
> As far as i understood g_rms gives only rmsd of the same structure in different configurations, but it doesn't fit homologous protein structures? 

Yep.

> In Option -f2 can i provide a trajectory of a homologous protein structure of it also have to be a reserence structure trajectory (which is provided in -s)?

You can provide anything that will allow for a meaningful 1:1 
correspondence of atomic sites. Depending how homologous these proteins 
are, you might need to use trjconv to strip out side-chains, leave only 
alpha-carbons, trim the terminal residues or such. Once you have ordered 
sets of numbers of the same size you can get a meaningful number out of 
g_rms.

Mark