Re: [AMBER] Altering ligand positions in Xleap

From: David A Case <>
Date: Tue, 16 Feb 2021 08:17:44 -0500

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.

AMBER mailing list
Received on Tue Feb 16 2021 - 05:30:04 PST
Custom Search