[gmx-users] protein ligand faraway from one another

[Justin Lemkul]

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

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
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==================================================