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

From: Vaibhav Dixit <>
Date: Thu, 23 Jan 2020 10:39:14 +0530

Thank you Prof. D. Case.
I'll watch out for the points you have mentioned while going ahead with
this approach.
Best regards

On Wed, Jan 22, 2020 at 6:36 PM David Case <> wrote:

> On Wed, Jan 22, 2020, Vaibhav Dixit wrote:
> >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?
> I'd keep the N1/N9 atoms of the bases, and give it a try.
> Presumably(?), the guanine tetrads will be unchanged. However, there
> are lots of topological ways that the "connecting" bases can be
> arranged. Unless you know that your unknown structure has the same
> general arrangement as your input structure, you could generate a
> structure that is entirely wrong.
> ....dac
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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,
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Received on Wed Jan 22 2020 - 21:30:02 PST
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