[gmx-users] protein ligand faraway from one another

[Fakhar Alam]

i use this tutorialGROMACS TutorialLysozyme in Water

*Justin A. Lemkul, Ph.D.*

*Department of Pharmaceutical SciencesUniversity of Maryland, Baltimore*


This example will guide a new user through the process of setting up a
simulation system containing a protein (lysozyme) in a box of water, with
ions. Each step will contain an explanation of input and output, using
typical settings for general use.

This tutorial assumes you are using a GROMACS version in the 5.x series.

On Thu, Sep 28, 2017 at 3:11 AM, Du, Yu <duyu at sioc.ac.cn> wrote:

>
>
>
> > -----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.
>
> --
> Yu
> --
> Gromacs Users mailing list
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