[gmx-users] DNA virtual site with Charmm force field

Erik Marklund erik.marklund at chem.ox.ac.uk
Wed Jul 1 13:29:02 CEST 2015

Hi Terry,

Correct. The forcefields provided with gromacs do not have a complete set of parameters for making vsites for nucleotides. You can work them out from geometry and mass moments however.

Kind regards,

> On 1 Jul 2015, at 10:23, Terry <terrencesun at gmail.com> wrote:
> Hi all,
> I'm trying to use virtual sites in a DNA in water simulation with Charmm27
> force field. When feeding my pdb to pdb2gmx with this cammand "pdb2gmx -f
> my_DNA.pdb -vsite hydrogens', it gives me this error
> Fatal error:
> No vsite database NH2 entry for type NN1
> Is this not implemented or did I miss something? Any input would be
> appreciated.
> Regards
> Terry
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