[gmx-users] rmsd on homologous protein structure
Mark.Abraham at anu.edu.au
Fri Nov 7 00:56:25 CET 2008
Tatsiana Kirys wrote:
> 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?
> 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
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