[gmx-users] Position Restraints MD

[Justin Lemkul]

On 9/24/19 12:09 AM, ISHRAT JAHAN wrote:
> Thanks Justin Sir for the response. Actually I have done the MD simulation
> of protein in presence of metal w.o.t. applying any position restraints and
> during the trajectory analysis I found that most of the time metal atom
> will stay out of the protein on seeing in VMD. I wanted to see the effect
> of metal on that protein so , I applied position restraint on that  metal
> atom. Is is better to do so or I should apply distance restraint? Any help
> would be appreciated.

Make sure what you are seeing is not some PBC effect. If the metal 
really is diffusing out, you need distance restraints like I suggested 
before. Most force fields are extremely crude in their treatment of 
interactions with metals.

-Justin

> Thanks and regards
>
> On Tue, Sep 24, 2019 at 9:32 AM ISHRAT JAHAN <jishrat17 at gmail.com> wrote:
>
>> Thanks Justin Sir for the response.
>>
>> On Mon, Sep 23, 2019 at 4:18 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>> On 9/20/19 2:10 AM, ISHRAT JAHAN wrote:
>>>>    Dear all,
>>>> I am doing MD simulation of protein and metal atom. I had applied
>>> position
>>>> restraints on metal atom. I had applied it as follows- ( kindly correct
>>> me
>>>> if i am wrong)
>>>> first made an index of metal atom and generated the posre_ion.itp file
>>>> using gmx genrestr and then added the force and atom index into the top
>>>> file of protein in [position restraint] part. In full.mdp file , added
>>> the
>>>> line define= -DPOSRES.
>>>> Then performed full md. But when i calculated the rmsd of backbone its
>>>> value is found to be around 0.02 nm(very small). I do not know whether
>>>> restraints have been applied on metal or on the whole system.  Am I
>>> doing
>>>> it correct or not?
>>> Using -DPOSRES is the default keyword for enabling position restraints
>>> on the entire protein. Given your tiny RMSD, that should confirm it.
>>> Visualize your trajectory and you should see that the protein isn't
>>> moving.
>>>
>>> Applying an absolute restraint to a metal ion is a curious approach.
>>> What may end up happening is your protein will diffuse but the metal
>>> will stay behind. If you're trying to enforce some type of coordination,
>>> use distance restraints instead.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Office: 301 Fralin Hall
>>> Lab: 303 Engel Hall
>>>
>>> Virginia Tech Department of Biochemistry
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
>>> ==================================================
>>>
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>>
>> --
>> Ishrat Jahan
>> Research Scholar
>> Department Of Chemistry
>> A.M.U Aligarh
>>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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