[gmx-users] regarding rmsd calculaton

[shakuntala dhurua]

thank you sir

On Thu, Oct 31, 2019 at 3:37 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/31/19 6:02 AM, shakuntala dhurua wrote:
> > thank you sir, by this gmx trjconv -center -pbc mol the two chains are
> > coming closer but still rmsd result is high and fluctuating highly while
> > taking two chain at a time. please suggest me to calculate resonable rmsd
> > value for full protein
>
> If you have very flexible regions, the RMSD value will be high. That's
> not necessarily wrong. If you've corrected the imaging issue that led to
> spurious increases in RMSD, this is the actual value. Whether or not it
> makes sense to consider the dimer as a whole in RMSD is another issue,
> but it depends on what you want to calculate and you need to be
> judicious in your selections for fitting and calculation groups,
> especially in the case of flexible termini or disordered regions.
>
> -Justin
>
> > On Wed, Oct 30, 2019 at 7:52 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 10/30/19 9:39 AM, shakuntala dhurua wrote:
> >>> i have generated trr file for a protein containing two chains .during
> the
> >>> simulation two chains are going at two different sides of the box. so
> the
> >>> RMSD results are abruptly high (near 35-40 angstrom). To create a image
> >> of
> >>> one chain at the same side of other chain,i used the following command
> by
> >>> removing pbc
> >>> ==============
> >>> try1. trjconv -s .tpr -f .trr -o .xtc -pbc mol -ur compact
> >>> try2.trjconv -s tpr -f .trr -o .xtc -pbc nojump
> >>> try3. -f a.mdp -c a_cluster.gro -o a_cluster.tpr
> >>> try4  trjconv -s a.tpr -f .trr -o xtc -fit rot+trans
> >>> ==============================
> >>> still similar results are coming. but for each chain,RMSD value is
> >>> reasonable.
> >>> kindly suggest some way to calculate RMSD value for full protein
> >> Create an index group for one protein and use it to center the
> >> coordinates. This will re-wrap the whole complex into the central image.
> >> gmx trjconv -center -pbc mol
> >>
> >> -Justin
> >>
> >>> On Wed, Oct 30, 2019 at 4:59 PM rajat punia <rjtpunia at gmail.com>
> wrote:
> >>>
> >>>> make sure you superimpose the structures using -fit flag.
> >>>>
> >>>>
> >>>> On Wed, 30 Oct 2019 at 16:39, shakuntala dhurua <
> >> madhu.dhurua94 at gmail.com>
> >>>> wrote:
> >>>>
> >>>>> actually I am using insulin protein system, i have calculated rmsd
> but
> >>>> that
> >>>>> is too high which is approx 40 amstrong which is not supposed to be ,
> >> and
> >>>>> initially during energy minimization two chain go far away from each
> >>>> other.
> >>>>> I have used flag like trjconv -s .tpr -f .trr -o .xtc -pbc mol -ur
> >>>> compact
> >>>>> trjconv -s .tpr -f .trr -o .xtc -pbc nojump etc but still result is
> >> same
> >>>> .
> >>>>> so please suggest me to solve this problem.
> >>>>> --
> >>>>> 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.
> >>>>>
> >>>> --
> >>>> *Regards,*
> >>>> *Rajat Punia*
> >>>> *PhD Chemical Engineering*
> >>>> *IIT Delhi*
> >>>> *+91-9821210386*
> >>>> --
> >>>> 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.
> >>>>
> >> --
> >> ==================================================
> >>
> >> 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.
> >>
>
> --
> ==================================================
>
> 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.
>