Re: [AMBER] make complex

From: David A Case <>
Date: Mon, 9 Nov 2015 08:21:09 -0500

On Mon, Nov 09, 2015, Fatemeh Sadat Alavi wrote:
> I extract ligand ( that is heme for my system) and add oxygen to it.
> then I optimized by Gaussian software and after that I add to protein.
> yes, your talk is correct, tleap can't change coordination, but when I do
> optimization, my structure was changed for that has overlap by protein.

Before the final optimization you mention, is there bad overlap between the
protein and the ligand?

It is not clear why you are removing the ligand, doing a Gaussian
optimization, and putting the ligand back in. Also, it is unclear from your
email what you mean when you say "after that I add to protein": did you add
the entire heme-O2 ligand or just the O2 itself back to the protein? I would
recommend avoiding the Gaussian optimization, and just using the original
coordinates in the PDB file.


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Received on Mon Nov 09 2015 - 05:30:07 PST
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