[gmx-users] Trouble running simulations with Nitrogen

[Ali Ahmed]

Hi
Try this

http://erg.biophys.msu.ru/tpp/

Best

On Thu, Jul 19, 2018 at 10:54 PM, Joshua Cummings <
Joshua.Cummings at uon.edu.au> wrote:

> Hi Everyone,
>
>
> I'm currently trying to run some simulations that involve the absorption
> of N2 into a liquid solvent. I'm having some difficulty in generating the
> topology for N2. 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
> END
>
>
> 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? Should I use some other forcefield for N2?
>
>
> Thanks in advance everyone,
>
>
> JOSHUA Cummings
>
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