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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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