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 <jalem...@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 <rjtpu...@gmail.com> wrote: > > > >> make sure you superimpose the structures using -fit flag. > >> > >> > >> On Wed, 30 Oct 2019 at 16:39, shakuntala dhurua < > madhu.dhuru...@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-requ...@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-requ...@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 > > jalem...@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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.