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

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Wed, 22 Jan 2020 12:21:39 +0530

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.
AND
Assistant Professor,
Department of Pharmacy,
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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: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
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Received on Tue Jan 21 2020 - 23:00:02 PST