[gmx-users] Trouble running simulations with Nitrogen
aa5635737 at gmail.com
Fri Jul 20 06:27:15 CEST 2018
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
> HETATM 2 N6A HDZ 0 0.000 0.000 -0.553 1.00 0.00
> 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? Should I use some other forcefield for N2?
> Thanks in advance everyone,
> JOSHUA Cummings
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