[gmx-users] Most appropriate structure to compare to in g_rms

[Natalie Stephenson]

Hi all,

This probably seems a really obvious question, but I'm struggling to get my head around it.
I am performing simulations to determine the effect of mutations on key regions of the protein. I have a crystal structure which I am using as the WT construct, and have performed homology modelling to create the point mutations of interest.

I have used g_rms using the Production MD .tpr as the reference to look at the change in movement for key regions of the structure, comparing the degree of movement with the WT and mutated construct. Unfortunately, this does not necessarily tell me about changes occuring, for example, one key region is showing no change in RMSD however is displaced compared to that in the WT. Would it be better to use the WT EM.tpr as the reference structure for everything (i.e. compare everything to the WT crystal structure)? Obviously these topologies will have slightly different numbers of atoms etc. will this be a problem?

Is there a better method that I could use to accomplish what I'm doing?

Thank you so much for any help you can offer.

Natalie