during rdf calculation i used flag gmx rdf -n .ndx -o .xvg -f .xtc -s .tpr it prompt Specify a selection for option 'ref' then i had given one one reference group 17 then it appear Selection '17' parsed then any number of selections for option 'sel' again it apper Selection '19' parsed .how can i solve this rdf calculation please suggest me.
On Fri, Nov 1, 2019 at 8:40 PM shakuntala dhurua <madhu.dhuru...@gmail.com> wrote: > thank you sir > > On Thu, Oct 31, 2019 at 3:37 PM Justin Lemkul <jalem...@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 <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. >> >> >> >> -- >> ================================================== >> >> 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.