[gmx-users] pdb2gmx

Mark Abraham mark.j.abraham at gmail.com
Wed Oct 29 10:56:27 CET 2014


The .rtp files are used by pdb2gmx in order to recognize residues in the
face of what can be massive noise in the input file. It primarily matches
names of atoms and residues. It writes a coordinate and topology file whose
atom and residue ordering matches each other, and whose atom types will
permit parameter lookup from the force field data bases - atom and residues
names become fairly (completely? idk) unimportant at this stage. I imagine
it is possible to duplicate the same atom name within a residue for use
with grompp, but likely there's no tool that generates such input for
grompp, because they need unique atom names so they can bring order from
chaos. Please check out the instructions and examples in Chapter 5 of the


On Wed, Oct 29, 2014 at 1:11 AM, Eric Smoll <ericsmoll at gmail.com> wrote:

> 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
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