Re: [AMBER] generating g-quadruplex DNA structures from a sequence

From: Satyaseelan C <>
Date: Thu, 23 Jan 2020 14:23:24 +0530

Dear Vaibhav,
     I would like to suggest 3D-NuS web-server ( for custom modelling of nucleic
acids structures including G-quadruplexes with your sequence of interest.
You can find the contact details in 3D-NuS web-server. You can contact us
for any further information related to building G-quadruplexes.

Hope the suggestions will be helpful to you.


On Wed, Jan 22, 2020 at 12:23 PM Vaibhav Dixit <>

> Dear Amber community,
> In a project, I am required to generate g-quadruplex structures for
> sequences for which crystal structure data in not available.
> Using amber tutorial B1 like procedure it is very easy to generate a
> variety of normal DNA helix structures.
> But I can't find a similar procedure for generating g-quadruplex structure
> only from a sequence.
> Thus I'm wondering if an expert on the list can suggest how can I approach
> this requirement using AmberTools.
> Will it make sense if I use an existing quadruplex PDB entry of identical
> length and simply delete coordinates for the bases (keep sugar-coordinates)
> and change residue names to required base e.g. DG to DA?
> Will leap add standard (reasonable) coordinates for bases? Will these give
> a reasonably good starting point for E min, and regular MD procedure?
> Looking forward to getting valuable insights into this.
> Thank you and best regards.
> --
> Regards,
> Dr. Vaibhav A. Dixit,
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email:,
> P Please consider the environment before printing this e-mail
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*Thanks & Regards*
*C .Sathyaseelan *
*PhD Research Scholar*
*C/o Dr. Thenmalarchelvi Rathinavelan*
*Molecular Biophysics Lab*
*Dept. of Biotechnology*
*Indian Institute of Technology (IIT)*
*Kandi, Hyderabad, Telangana - 502285*
*Ph.No 8300150807, 9659750301*
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Received on Thu Jan 23 2020 - 01:30:01 PST
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