It depends on how the molecules are defined in the topology file. If the coordinates of both molecules are contained in the main part of the topology file, only one position restraint file is enough and it should contain entries for all the non-hydrogen atoms in both molecules. However, if the coordinates of only one of the molecules are in the main topology file, whereas the coordinates for the second molecule are read as .itp file (include file), or if both are read as include files, then there should be two position restraint files. If both molecules are built of building blocks (such as protein, DNA ...) then running separately pdb2gmx should generate adequate posre files for each of them. If one of the molecule is not built of standard building blocks (for instance, if it is a ligand, co-factor...) and you want nevertheless apply restraints to it in the simulation, then maybe the better solution is to write a short program (in C or FORTRAN) or script, which could filter out the numbering of non-hydrogen atoms.
I hope it can help Best regards Paulo Netz Universidade Federal do Rio Grande do Sul Porto Alegre, Brazil On Wed, Oct 17, 2012 at 6:46 PM, Arman M. Soufiani <armansoufi...@gmail.com>wrote: > Dear Gromacs users, > > It might seem a simple problem, however, I could not find a correct way to > define two restrained groups in my .mdp file. > If I include the following an error appears that notifies me that I am not > able to define two restraints! > > define = -DPOSRES_1 > define = -DPOSRES_2 > > Do I need to make an index for the collection of the atoms of both groups > and then use one define position restraint for them?! > If yes, I would be happy if you direct me how should I embed it in the .mdp > file? > > Regards > > Arman > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Restraining-two-Macromolecules-tp5002141.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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 > -- 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
