[gmx-users] Effect of a single mutation in a protein

Justin Lemkul jalemkul at vt.edu
Wed Mar 26 18:41:50 CET 2014

On 3/26/14, 10:57 AM, Pappu Kumar wrote:
> I did 50 ns MD simulation of WT and mutant protein in gromacs with
> Amber ff99sb. The mutation alters the function of the protein. The RMSD
> and RMSF differences in WT and mutant are <1 A. I also calculated the change in entropy of the water molecules around 4 A by
> Schilter's formula which seems to change in case of the mutation. Let me know how to
> calculate the H-bonding lifetime of the water during the simulation.

g_hbond has options to do this; see g_hbond -h.

> Further I plotted the PC1 of C-alpha atoms of WT with the PC1 of the
> mutant. I am wondering if it makes sense to compare PC1 from different
> trajectories. Please suggest me some possible analysis. Thank you.

Only if those PC's are comparable; more interesting would likely be projecting 
the configurations of the mutant simulation on WT PC1 to see the overlap in 
phase space.



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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