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

Justin Lemkul jalemkul at vt.edu
Mon Aug 18 18:47:45 CEST 2014

On 8/18/14, 9:41 AM, Natalie Stephenson wrote:
> 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.

Can you provide your exact command(s) and the groups chosen for fitting and 
output?  The outcome is highly dependent upon proper choices being made.

> 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?

This will be a problem.  You can get around it, though, by using tpbconv (gmx 
convert-tpr in 5.0) to extract just backbone atoms from both .tpr files and 
trajectories.  If you don't, g_rms will complain about mismatching atom numbers 
or you will be mapping the wrong atoms in the trajectory since the two proteins 
have different numbers of atoms.

Also note that g_rmsf is probably useful here, too, as you can get per-residue 
fluctuations and RMSD.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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