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

Pappu Kumar papuu_k at yahoo.com
Thu Mar 27 19:47:42 CET 2014

Thank you. Regarding g_anaeig, I basically took the eigenvectors of C-alpha atoms of one trajectory and then projected the other trajectory on it.

I obtained the ATP parameters from a paper. Like all simulations, MD has some limitations. So I don't want to highlight the things which may not be correct. 

There is no unfolding. Also the gibbs energy surface projected on PC1 and PC2 looks quite different than RMSD vs. Rg surface calculated by g_sham (also the lowest energy structures.)

Can I calculate del del G by TI? I am not sure how to define the reaction coordinates. Is it a good idea to do umbrella sampling between two states to determine the free energy?

On Thursday, 27 March 2014 8:35 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

On 3/26/14, 2:24 PM, Pappu Kumar wrote:
> I have already used g_hbond. I am not sure how accurate is the H-bond lifetime calculation. Also the trajectory snapshots need to be saved quite often. Could you tell me how to interpret output from g_hbond -ac :

There should be references provided in the g_hbond output when calculating 
lifetimes.  At the very least, they're in the manual.  So you can determine for 
yourself how reliable the outcome is.

> @ s0 legend "Ac\sfin sys\v{}\z{}(t)"
> @ s1 legend "Ac(t)"
> @ s2 legend "Cc\scontact,hb\v{}\z{}(t)"
> @ s3 legend "-dAc\sfs\v{}\z{}/dt"

Plotting these data sets in XmGrace will clear things up.

> Could you tell me how to  project the configurations of the mutant simulation on WT PC1? Are you aware of any paper where I can read more about it? Can I compare the PC1 vs PC2 in case of WT and mutant?

See g_anaeig -h, as well as previous discussions in the list archive on doing this.

> I am trying to find out how such mutation buried inside the protein away from the ligand binding pocket can influence the function of the protein. I actually see some changes in the positon of the bound ATP in the mutant compared to the WT. But I am not sure how reliable it is due to the inaccuracies in parameterization.

Well, if your parametrization is inaccurate and you know it is, what use are the 
simulations?  Or are you just wondering if there is a possibility of 
inaccuracies?  Either way, that's something that should be sorted out long 
before doing any real simulations :)

> I also calculated the Gibbs free energy landscape by g_sham using Rg and RMSD. The value varies from 0-6.5 kJ/mol in both cases but the regions with ~0 kJ/mol has changed.

Do the proteins unfold?  If not, I doubt Rg vs. RMSD is a very sensitive metric 
of anything.  You can, of course, map back the locations of the energy minima to 
see if there are any interesting differences there, but such a plot (Rg vs. 
RMSD) is probably only useful in protein (un)folding simulations.



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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