[gmx-users] Generating N2 topology

Joshua Cummings Joshua.Cummings at uon.edu.au
Wed Jul 4 08:01:42 CEST 2018

Hi All,

I'm currently trying to generate the topology for molecular Nitrogen (N2) and am running into some trouble. For reference, the pdb file I have for N2 is as follows:

HETATM    1  N6B HDZ     0       0.000   0.000   0.553  1.00  0.00           N
HETATM    2  N6A HDZ     0       0.000   0.000  -0.553  1.00  0.00           N
CONECT    1    2
CONECT    2    1

When I try to generate the .itp file and topology via pdb2gmx (OPLS), gromacs doesn't recognise the residue. I've tried using both the LigParGen server and the PRODRG to generate the topology, but neither work. PRODRG generates an error saying it does not deal with mono/di-atomic molecules and LigParGen won't recognise N2 at all.

I haven't had any trouble generating topologies for other small gas molecules such as CH4, am I missing something here or are OPLS parameters not possible for N2?

Thanks everyone,

JOSHUA Cummings
PhD Candidate
BSc (Chem)(Hons)
The Priority Research Centre for Frontier Energy Technologies and Utilisation
School of Chemical Engineering
Newcastle Institute for Energy and Resources (NIER)
T: +61 (0)2 4033 9244
M: +61 (0)4 2325 7078
E: Joshua.Cummings at uon.edu.au
The University of Newcastle (UON)
University Drive
Callaghan NSW 2308

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