[gmx-users] regarding rmsd calculaton

[shakuntala dhurua]

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

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.
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> >>
> >> --
> >> *Regards,*
> >> *Rajat Punia*
> >> *PhD Chemical Engineering*
> >> *IIT Delhi*
> >> *+91-9821210386*
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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