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
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 > _______________________________________________ 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
