On 9/19/13 10:12 AM, fatemeh ramezani wrote:
dear users
I'm studying gold nano-particle effect on one of the blood protein stability
and structure. one time I simulated the protein in the presence of the gold
nanoparticle and once without nanoparticles.
when I simulated protein alone in water, I expected the protein to remain
stable but protein RMSD, gyration,dssp and .... graphs show protein structure
is changing and protein helices are opening during the simulation.
Thus, I can not study nanoparticle interaction effect on the protein
structural changes , because the structural changes also observed in the
absence of nanoparticle.
I think there is a problem. What is the solution you offer me? What is the
problem?
If the model does not reflect reality, that suggests a deficiency in the force
field, run settings, or system setup. Since you've told us nothing about how
you're doing the simulations, there's little advice anyone can offer.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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