[gmx-users] Protein ligand complex simulation

[Justin Lemkul]

On 4/3/17 8:05 AM, RAHUL SURESH wrote:
> The ligand is out of protein in the very first frame of production run.
>  Then that should be my docking error.?
>

It sounds like your starting configuration was prepared incorrectly (however you 
manipulated it to prepare the system) or this is a PBC effect.

-Justin

> On Mon, 3 Apr 2017 at 5:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 4/3/17 7:56 AM, RAHUL SURESH wrote:
>>> Dear Justin
>>>
>>> First I apologise for the error I had made in my previous mail. It's
>> during
>>> production.
>>>
>>> I have recentered it. The ligand is out of the protein. The ligand is not
>>> in position where I docked.
>>>
>>
>> Then watch the recentered trajectory to see what happened.  Dissociation
>> should
>> be apparent, and smooth if the PBC effects have been correctly accounted
>> for.
>> If the dissociation is real, either the initial position was unfavorable
>> (docking is sometimes incorrect!) or the topology of the ligand was
>> inadequate
>> and thus you got a poor model of the interactions.
>>
>> -Justin
>>
>>>
>>> On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>>
>>>>
>>>> On 4/1/17 8:59 AM, RAHUL SURESH wrote:
>>>>> I followed the complex simulation tutorial. Minimisation for 2ns
>>>>>
>>>>
>>>> FYI there is no time during energy minimization, so you did not do "2
>> ns"
>>>> of
>>>> minimization.
>>>>
>>>>> I used auto dock to dock ligand with protein. During simulation I find
>>>> the
>>>>> ligand out of protein. Is that usual?
>>>>>
>>>>
>>>> This is probably a periodicity effect.  There's no way during the
>> course of
>>>> minimization that a ligand-protein complex can completely dissociate.
>> Use
>>>> trjconv to make sure you've properly re-imaged the system.  A simple
>>>> recentering
>>>> should do it.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 629
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
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>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>> Gromacs Users mailing list
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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