[gmx-users] Unstable Alpha Helix

[Justin Lemkul]

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.

-Justin

> 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 ?
>
> Regards,
> Amit
>

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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