sure. thanks
On Sun, Oct 18, 2009 at 10:45 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > sunny mishra wrote: >> >> oh cool. I have gromacs version 4.4 so my protein will be on the x >> axis by default and to orient the long axis of protein along z axis >> then I have to editconf it and then rotate the final structure to 90 >> degrees along y axis, right? reply will be highly appreciated >> > > Try it and see. You learn more by doing, and anyway, it takes about 10 > seconds to run editconf, instead of waiting for a reply seeking affirmation. > > -Justin > >> Thanks, >> >> Sunny >> >> On Sun, Oct 18, 2009 at 10:18 PM, Justin A. Lemkul <jalem...@vt.edu> >> wrote: >>> >>> sunny mishra wrote: >>>> >>>> Dear All, >>>> >>>> I am following the tutorial given by justin and have question >>>> regarding the orientation of protein. Tutorial says that orient the >>>> protein along z axis using editconf -princ command followed by the >>>> rotation along y axis. My question is that when I use the editconf >>>> -princ command, does it automatically orient the protein along z axis >>>> because i gave the following command and I wasn't sure if I am correct >>>> or not, the command is: editconf -f protein.gro -princ -o >>>> protein_z.gro >>>> >>> It depends on your Gromacs version. As stated in the tutorial: >>> >>> "The .pdb file was oriented along the z-axis using editconf -princ, >>> followed >>> by a rotation about the y axis. Note that in Gromacs-3.3.x, the -princ >>> option oriented the long axis of the structure (in this case, the helix >>> axis) along the z-axis by default, but this option has changed as of >>> Gromacs-4.0.4, which orients the long axis along the x-axis. If you want >>> to >>> skip the construction of this peptide, the properly oriented structure >>> can >>> be found here." >>> >>>> Please correct me if I am wrong and also what do you mean when you say >>>> followed by the rotation along the y axis, by how much angle do i need >>>> to rotate? >>>> >>> What angle do the coordinate axes make with one another? :) >>> >>> -Justin >>> >>>> Thanks, >>>> >>>> Sunny >>>> _______________________________________________ >>>> gmx-users mailing list gmx-us...@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search before >>>> posting! >>>> Please don't post (un)subscribe requests to the list. Use the www >>>> interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> _______________________________________________ >>> gmx-users mailing list gmx-us...@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
