[gmx-users] Position Restraints MD

[ISHRAT JAHAN]

Thank you sir for the valuable suggestions. I have done distance restraints
on metal and some atoms of amino acids residue as follows-
first generated the distance restrained .itp file using the command
gmx genrestr -f file.gro -n asp83_OD1_Zn.ndx -o distance_restrain.itp
-disre_dist 0.221 -disre_frac 0.221 -disre_up2 0.221 -fc 1000 1000 1000
where 0.221 is the bond length between the OD1 and Zn, and similarly
generated itp files for other atoms also and then added thes files in the
.top file by changing the residue no. accordingly.
perform full md but after the simulation run when i calculated the pairwise
distance between these atoms it shows large fluctuations nearly 0.4 nm.
Please tell whether position restraints have been applied on required atom
or not. If this is not the correct procedure kindly tell the correct
procedure.
Regards

On Wed, Sep 25, 2019 at 12:17 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
> >>>
> >>> ==================================================
> >>>
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>> posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-request at gromacs.org.
> >>>
> >>
> >> --
> >> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


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