Hello Gromacs users, I would like to add a molecule as a "residue" in the aminoacids.rtp file and I have a few questions.
As far as I understand, a residue in a gro file can multiple atoms with the same "atom name." What links every atom in this residue to parameters in the top [ atoms ] directive is the *order.* The gro file "atom names" must match the top file atoms names but the mapping of parameters is done via the order, correct? This allows atoms in a residue to have the same "atom name" but be associated with a different "atom type," "charge group," etc... Does an entry in a residue database (e.g., aminoacids.rtp) work the same way? The syntax is shown below. [ TEST ] [ atoms ] ; atom_name atom_type atom_charge charge_group I have to specify the "atom name," force field "atom type," "atom charge," and "charge group" for every atom in the "TEST" residue in order. The "atom name" must match the "atom name" in the input coordinate file but the mapping is applied by the entry order, correct? I do no need unique "atom names," correct? Best, Eric -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
