Re: [AMBER] Altering ligand positions in Xleap

From: Gordon Richard Chalmers <>
Date: Tue, 16 Feb 2021 13:20:46 +0000

Just a quick relevant comment. You may want to try the Oculus Nanome
software if have access to it. It is quite interesting in 3D to use this for
your purpose.

Gordon Chalmers
From: David A Case <>
Sent: Tuesday, February 16, 2021 8:17 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Altering ligand positions in Xleap


On Tue, Feb 16, 2021, Sruthi Sudhakar wrote:

>I am currently working on a G- Quadruplex ligand system. We have used the
>docked structure of the ligand as a starting structure for the dynamics.
>But now we need to place the ligand on top of a particular guanine
>initially to see how the system changes over time. I wanted to know if it
>is possible to place the ligand closer to the particular residue of the
>macromolecule in xleap? If yes could someone kindly guide me regarding the

xleap is not a very good program for this purpose: it has a rather
two-dimensional view of making changes. I'd recommend other visualization
packages (Avogadro, Chimera, VMD, coot...) that allow you to select the
ligand, and interactively move it into the position you want.

...good luck....dac

p.s. I don't do this a lot, and I'm sure I've missed some good structure
editors. I hope others on the list will chime in with recommendations.

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Received on Tue Feb 16 2021 - 05:30:05 PST
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