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 -- ================================================== 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 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
