[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.

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.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
ORCID ID: https://orcid.org/0000-0003-4015-2941
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Received on Tue Jan 21 2020 - 23:00:02 PST
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