hi justin, will try that ....
thanks Ram On Thu, Mar 4, 2010 at 4:51 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > ram bio wrote: >> >> HI Justin, >> >> Thanks for the info. >> >> I have followed your tutorial earlier, it really works, and that was >> for 1 protein, but if 2 or more different kinds of proteins are to be >> inserted then how to generate the a single topology file for all the >> proteins using pdb2gmx and also can you please let me know the other >> ways to insert the proteins in lipid bilayers.... >> > > You don't need a single topology for all the proteins. Instead you can > generate individual topologies for each protein with pdb2gmx, remove the > unnecessary #includes, [system], and [molecules] directives to make them > single-molecule .itp files, and then simply: > > #include "protein_A.itp" > #include "protein_B.itp" > > in your .top file. > > Other ways to insert proteins might include using genbox creatively, VMD, > g_membed, etc. Search the list archive. > > -Justin > >> >> Ram >> >> On Thu, Mar 4, 2010 at 4:36 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> ram bio wrote: >>>> >>>> Dear Gromacs Users, >>>> >>>> I would like to run molecular dynamics by inserting multiple proteins >>>> in the same lipid bilayer using gromacs, is it possible? if so, please >>> >>> Just about anything is possible :) >>> >>>> let me know if any tutorial is available or any kind of help is >>>> available.... >>>> >>> There is a tutorial for a basic membrane protein system linked from the >>> Gromacs tutorials page. As for inserting multiple proteins in the >>> membrane, >>> there are several ways to do it, but if you want to use InflateGRO, >>> you'll >>> need the latest version: >>> >>> http://www.csb.bit.uni-bonn.de/inflategro.html >>> >>> -Justin >>> >>>> Thanks in advance, >>>> >>>> Ram >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> 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 > MILES-IGERT Trainee > 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
