Where should I place, in topol.top, the [defaults] section in ligand .top file created by ACPYPE

User discussions
1

GROMACS version: 2023.1
GROMACS modification: No

Dear all,

It’s been a long time since I’ve run GROMACS simulations, and I am preparing calculations for a pretty complex system (for me) – a polymerase with one deoxy-adeonosine triphosphate (DTP) + three Mg 2+ ions in the active site and a DNA molecule. The force field is Amberf99SB.

I have parameterized the DTP using ACPYPE (latest version from the conda repo), and it contains a section called [ defaults ]:

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333

Is it crucial that I include this entry in the topol.top file? If so, where should I place this entry?

I’ll gladly attach my files if this helps.

Best regards,

Marcos Verisssimo Alves
Lund University, Sweden / Universidade Federal Fluminense, Brazil

2

Ligand topologies should not have a [defaults] directive. These are the master instructions for the force field and should only ever be present in forcefield.itp. Many programs generate what are essentially standalone force field files for species, assuming they will be used by themselves. You need to remove [defaults] and any system-level directive (like [system], [molecules], etc.) from the ligand topology so it can be incorporated into the system topology without syntax errors.

3

Dear Justin,

Thank you for the answer. I’m glad I did the right thing – not including it anywhere :-) . Now I can proceed with confidence that at least ignoring [defaults] will not be a source of error in my MD.

Best,

Marcos