[gmx-users] pdb2gmx

Eric Smoll ericsmoll at gmail.com
Wed Oct 29 01:11:27 CET 2014

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
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?


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