In this case, Can't you just use pdb2gmx to regenerate the topology file from the merged gro which will resolve the separate moleculechains for you?
On 2011-03-30 04:25:34AM -0500, Mark Abraham wrote: > On 30/03/2011 8:14 PM, Ghassen Hassani wrote: > > Dear Friends, > Right now i am working on the docking of a small ligand to a receptor. in > order to begin md simulations in gromacs, i need to create some files.. > > I have already docked my ligand to the receptor and i have those files: > - ligand_receptor.gro > - posre.itp (for only the receptor !!) > > > I have 2 Questions: > > 1- How can i expand the posre.itp file to also include the ligand.data ? > > > Don't. The position restraints file is intended to be #included from within a > [moleculetype]. You have two, so you need two position restraint files, each > #included from a different, appropriate place. The GROMACS tool genrestr can > help generate that for the ligand. > > that means how can i do to create a posre.itp-file for my > ligand_receptor-komplex ? > > > Don't. > > > 2- I have 2 separate top-files: ligand.top (from the prodrg-server) and the > receptor.top file. How can i "merge" the 2 files and obtain the file > ligand_receptor.top for the whole ligand-receptor-komplex ? > > > You need to convert one of your [moleculetype] definitions in one of your > .top files into an .itp file > (http://www.gromacs.org/Documentation/File_Formats/.itp_File) and #include it > suitably from the other. See chapter 5 of the manual for details. This is > tricky, do your homework first. Note that you should take note of the warning > here: http://www.gromacs.org/Downloads/Related_Software/PRODRG > > > > > > > Many thanx, please email-me on my adress: > greendreams1...@yahoo.de<mailto:greendreams1...@yahoo.de> > > Yours. > > > > > > No, that is against accepted netiquette. If your question is worth answering, > then that answer is worth broadcasting and archiving so others can learn from > it. > > Mark > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- =============================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | =============================================================== -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
