[gmx-users] Unstable Alpha Helix

[amitbehra at chemeng.iisc.ernet.in]

Hello Justin,
I am using "stride" program to analyze the helices.
Can the Potential switch and other mdp parameters affect the stability of
an Alphahelix.

Regards,
Amit
> Date: Mon, 19 Dec 2016 08:06:29 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Unstable Alpha Helix
> Message-ID: <78b951a1-4cb3-e4fc-4239-cc19fd03c9a5 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> 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
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