Hi Try this http://erg.biophys.msu.ru/tpp/
Best On Thu, Jul 19, 2018 at 10:54 PM, Joshua Cummings < joshua.cummi...@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 > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.