[gmx-users] protein ligand faraway from one another

[Fakhar Alam]

I use the protein-ligand complex tutorial but still the protein and
legend far away from each other.

On Sat, Oct 7, 2017 at 9:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/7/17 6:03 AM, Fakhar Alam wrote:
>
>> 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.
>>
>
> If you've got a protein-ligand complex, you should probably be looking at
> the protein-ligand complex tutorial :)
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
> -tutorials/complex/index.html
>
> -Justin
>
>
> 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
>>>> --
>>>> Gromacs Users mailing list
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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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>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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