[gmx-users] protein ligand faraway from one another

[Justin Lemkul]

On 10/7/17 2:31 PM, Fakhar Alam wrote:
> I use the protein-ligand complex tutorial but still the protein and
> legend far away from each other.

You're not providing any useful information towards a solution. What was 
your starting structure? Did you start with a docked/crystallized 
complex? Did you follow the tutorial's instructions in preserving the 
coordinates, and not allowing whatever parametrization server/method to 
alter the coordinates? At what stage are you observing this separation, 
and could it be a PBC effect?

Your exact commands and observations are necessary, otherwise there is 
no way to help you arrive at a resolution.

-Justin

> 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
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>
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>>>>>
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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.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================