[gmx-users] RMSD comparison to a different reference structure.

[Natalie Stephenson]

Hi,

I was wondering if you would be able to advise me of the best method to compare a mutated and WT structure. I was hoping to perform RMSD analysis for certain regions within a mutation against the same region within the wild type structure. Unfortunately, the atom numbering is likely to be off for some regions, as the mutation with add/remove atoms. As only one index file is specified for the g_rms command I wondered how best to do this? Or if it was possible?

Thanks,
Natalie