[gmx-users] conformational change

Justin Lemkul jalemkul at vt.edu
Thu Dec 13 19:04:57 CET 2012

I see no reason why water molecules would induce conformational change, and if 
you delete the starting waters, probably more will just leak in as is the case 
in many beta-barrel proteins.  Such changes are more a function of the force 
field and its proper use via .mdp settings.  Note that metrics like RMSD and 
radius of gyration are relatively poor metrics of such behavior.  Unless you're 
measuring just the RMSD of the problematic peptide segment, the magnitude of 
change is likely masked by the size of the remaining protein.  The radius of 
gyration is unlikely to change unless the whole protein shows extensive unfolding.


On 12/13/12 12:23 PM, Shine A wrote:
> Sir,
>          I am studying the dynamics of a beta barrel shaped membrane
> protein. The starting end of the barrel is a helix which is inside the
> barrel. During salvation with genbox some water molecules entered inside
> the barrel.Then I did the 20 ns dynamics.After dynamics more number of
> water molecules trapped inside the barrel. I convert the output gro file
> into pdb and viewed using pymol. Then I noticed that the starting helix
> part is changed in to loop.Then I calculated the rmsd deviation and radius
> of gyration, it not showing any characteristic deviation.Is water molecule
> change the conformation of helix inside the barrel? Is it necessary to
> delete all the water molecules inside the barrel before dynamics? then
> how?


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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