[gmx-users] Fwd: Can a mutation make a protein stable - result analysis from GROMACs run

Justin Lemkul jalemkul at vt.edu
Thu Sep 14 01:37:45 CEST 2017

On 9/11/17 5:33 PM, Deep kumar wrote:
> Hello All,
> I ran a 10ns simulation on a wild and mutant type of a protein complex.
> Attached is the rmsf graph. "Green" is the mutant protein with mutation at
>   residue 71 (marked) and "purple" is the wild protein. After looking at the
> graph can it be said that the mutant has made the complex more stable? How
> possible is this scenario? I am yet  to do dssp analysis and h-bond
> analysis. Can someone tell me what other analysis can be useful for this
> case?

Lots of things may be useful, but it depends on the nature of the 
protein and its composition.  No one here is going to be able to tell 
you what to do, nor is that the purpose of this list.  Research what is 
known about your system, think about its architecture and interactions 
within itself.

10 ns is not nearly enough data to conclude anything meaningful.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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