Empty Bonded Parameters in the Topology

User discussions
1

GROMACS version: 2019.2
GROMACS modification: Yes/No

Dear All,

I am simulating a protein in water. After pdb2gmx, I realized that some bonded parameters are empty in the topol.top file. Relevant part of the topology is as follows
[bonds]
………….
58 59 2 gb_32
59 336 2
60 61 2 gb_5
………….

[angles]
………………
57 58 59 2 ga_16
58 59 336 2
57 60 61 2 ga_30
……………………

[dihedrals]
…………………….
55 57 60 62 1 gd_40
57 58 59 336 1
58 59 336 335 1
57 60 62 64 1 gd_14
…………………………

Atoms without gb, ga and gd correspond to the Cys residues; that is disulfide bond between two Cys residues and related angles, dihedrals.

The question is why are the corresponding slots empty? Do I have to manually enter relevant information (for ex: gb_36, ga_6, gd_26 and gd_21)?

Thanks in advance,
Deniz

2

Any parameter values not explicitly defined in the topology will be referenced from ffbonded.itp.

3

Thank a lot.