[gmx-users] Unstable Alpha Helix
jalemkul at vt.edu
Mon Dec 19 14:08:10 CET 2016
On 12/19/16 7:01 AM, amitbehra at chemeng.iisc.ernet.in wrote:
> Hello everyone,
> I am trying to simulate an Alpha helix inside a bilayer. But a part of the
> alpha helix is loosing its form and converting into turns( while
> alphahelix should be stable in the bilayer environment)
How are you assessing this? DSSP? Dihedral time series? Note that simple
visualization is often misleading. Helices can still be helices, even if the
program you're looking at disagrees.
> I am using Amber-99sb-ILDN for the protein and Slipids for the bilayer.
> I am using Potential-switch for VdW and PME for electrostatics.
> Does these parameters affect the form of the Alphahelix ?
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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