Re: [AMBER] ligand split

From: David Case <>
Date: Tue, 14 Jan 2020 19:25:48 +0000

On Tue, Jan 14, 2020, MYRIAN TORRES RICO wrote:
>I'm looking for any idea about a problem with my results. I have
>launched a molecular dynamic of my complex ligand-protein (my ligand
>is a tetrasaccharide), and when finished all steps (minimization,
>heat, pressure and volume), my molecule is split.

I'm guessing this means that some bond is missing in the carbohydrate
part. You'll probably see what is happening even after the minimization
step. Visualize the minimized structure and see which bonds are
"broken"; use parmed to check the prmtop file for the presence/absence
of bonds between the parts of the ligand that are no longer "together".

Then, you will need to figure out what went wrong. It's a good idea to
set up just the ligand, and run a minimization on it. That gives you a
lot fewer things to look at.


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Received on Tue Jan 14 2020 - 11:30:01 PST
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