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 shin...@iisertvm.ac.in
Subject: [gmx-users
literature to make sure the ff you are using is not biased
against (or in favor) of helical structures.
Best regards.
Message: 4
Date: Fri, 14 Dec 2012 09:50:28 +0100
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [gmx-users] conformational change
To: Discussion list for GROMACS users
recent literature to make sure the ff you are using is not
biased against (or in favor) of helical structures.
Best regards.
Message: 4
Date: Fri, 14 Dec 2012 09:50:28 +0100
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [gmx-users] conformational change
To: Discussion list
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
I see no reason why water molecules would induce conformational change, and if
you delete the starting waters, probably more will just leak in as is the case
in many beta-barrel proteins. Such changes are more a function of the force
field and its proper use via .mdp settings. Note that
are that it still is a helix.
Best regards.
Message: 4
Date: Thu, 13 Dec 2012 22:53:30 +0530
From: Shine A shin...@iisertvm.ac.in
Subject: [gmx-users] conformational change
To: gmx-users@gromacs.org
Message-ID:
CAEUDBJr1nBB2We-rJzg0H9er9Bf0cEgqn4mgwratJyPff=A0=g...@mail.gmail.com
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