[gmx-users] conformational change

Julio Dominguez acheron24 at hotmail.com
Fri Dec 14 06:32:46 CET 2012

Hello Shine,

Besides what Justin mentioned you have to be careful of what you consider a helix or a loop. Pymol is note very accurate when it assigns secondary structure. I recommend you install dssp within Pymol (see here and here) and double check you secondary structure. Odds are that it still is a helix.
Best regards.
> Message: 4
> Date: Thu, 13 Dec 2012 22:53:30 +0530
> From: Shine A <shine.a at iisertvm.ac.in>
> Subject: [gmx-users] conformational change
> To: gmx-users at gromacs.org
> Message-ID:
> 	<CAEUDBJr1nBB2We-rJzg0H9er9Bf0cEgqn4mgwratJyPff=A0=g at mail.gmail.com>
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> 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?


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