Re: [AMBER] make complex

From: case <>
Date: Sun, 8 Nov 2015 12:50:42 -0500

On Sun, Nov 08, 2015, Fatemeh Sadat Alavi wrote:
> my protein consists Heme (ligand) when I want to change ligand, for example,
> adding oxygen.

> I extract it from PDB and change I do optimization and after save it.
> when I do tleap, the complex is incorrect, I see the protein and ligand have
> overlap together.

We need many more details. What is the "it" that you extracted from the PDB?
How did you change it; how did you optimize it?

Note the tleap doesn't change the coordinates you give it. So if the protein
and ligand overlap after tleap, it is highly probable that they overlapped
before the tleap step.


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Received on Sun Nov 08 2015 - 10:00:03 PST
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