Re: [AMBER] make complex

From: Jason Swails <>
Date: Mon, 9 Nov 2015 07:56:23 -0500

On Mon, Nov 9, 2015 at 3:03 AM, Fatemeh Sadat Alavi <>

> I extract ligand ( that is heme for my system) and add oxygen to it.
> then I optimized by Gaussian software

‚ÄčThis is your problem. This changes the coordinates and is clearly causing
it to overlap with the protein.

> 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.

If you cannot find a way to prevent the heme from overlapping (perhaps by
using cpptraj to align the optimized heme structure with the original using
the rmsd command), then do not use the optimized coordinates when adding it
to the protein.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 09 2015 - 05:00:04 PST
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