Re: [AMBER] regarding G-quadraplex

From: Bill Ross <>
Date: Mon, 24 Dec 2018 05:12:36 -0800

I'd look for existing PDB files. Also I'd ask anyone who has modeled the
G-4 you want. Think about the different kinds of quads and loops
(directionality etc.). If you can get your G's, it's also easy enough to
add loops and flap them into something reasonable with dynamics.

Failing that, one logical but not often mentioned possibility in leap
would be to impose the angles from the literature on a 4-G strand
generated using 'sequence'. In that case, you'd get 4 strands of 4-G's,
assemble them graphically unless you have a better way, then generate
the loops, bend them (how depends on the graphics program), bond them
into place and/or do whatever it takes with cutting and pasting to get a
PDB file with the residues in reasonable order, and a TER 'card' after
each strand. The higher-end your graphic editor, the easier it might be.


On 12/24/18 4:31 AM, Charu Sharma (JRF) wrote:
> Respected All,
> i want to know how to create the G- QUADRAPLEX STRUCTURE ?
> _______________________________________________
> AMBER mailing list

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Received on Mon Dec 24 2018 - 05:30:02 PST
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