I have used principle function in Amber to get the principle axis of DNA as in attached photo. But I don’t know how to use this out put file in align during simulation ??
Best regards,
Mohamed Marzouk Sobeh
Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
T.A Physics department,Ain Shams University, Cairo, Egypt.
Emails:
mohamed_marzouk.sci.asu.edu.eg
marzouk.aa.m.titech.ac.jp
marzouk_biophysics.yahoo.com
mohamedmarzoukphysics.gmail.com
Mob. and WhatsApp.:
+81 070-4070-9549
+2 01061417414
> On Apr 27, 2020, at 10:47 AM, mohamed marzouk <mohamedmarzoukphysics.gmail.com> wrote:
>
> Dear Amber users
> I am trying to do dissociation for protein DNA complex, However the protein slide over the DNA, so that I want to do cylindrical simulation to get direct dissociation or other way of dissociation. This cylindrical Simulation based on the distance between the Z-axis (I want DNA to be that axis) and the center of mass of protein (this distance is the r in cylindrical coordinates ) to do so
> I want to know ?
> How can I define the axis of DNA ?
> Can I keep this axis fixed by restrain of ends of DNA (3 residues from each side)?
> Any idea about cylindrical Simulation?
>
>
> Best regards,
> Mohamed Marzouk Sobeh
> Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
> T.A Physics department,Ain Shams University, Cairo, Egypt.
> Emails:
> mohamed_marzouk.sci.asu.edu.eg
> marzouk.aa.m.titech.ac.jp
> marzouk_biophysics.yahoo.com
> mohamedmarzoukphysics.gmail.com
>
> Mob. and WhatsApp.:
> +81 070-4070-9549
> +2 01061417414
>
>
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Received on Tue Apr 28 2020 - 23:30:02 PDT
