[gmx-users] protein ligand faraway from one another

Du, Yu duyu at sioc.ac.cn
Thu Sep 28 12:12:01 CEST 2017

> -----Original Messages-----
> From: "Fakhar Alam" <fakharalamchemistry at gmail.com>
> Sent Time: 2017-09-28 16:07:52 (Thursday)
> To: gmx-users at gromacs.org
> Cc: 
> Subject: [gmx-users] protein ligand faraway from one another
> Dear Gromacs Experts,
> I am doing simulation of protein-ligand complex. However when I follow the
> steps in the tutorial, the ligand is very faraway from the protein. How can
> I put the ligand close to the protein ?
> Thanks,
> Alam
> -- 
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Before simulation, the protein and ligand is a complex, right?

Can you give the detail of which tutorial you are following and which step have you followed to?
Do you follow the tutorial exactly or tune some factors that can impact the interaction between protein and ligand?
I have never encountered the problem. We need more information to answer your question.


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