[gmx-users] Position Restraints MD

[ISHRAT JAHAN]

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.
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
>


-- 
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh