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

[Terry]

Hi Erik,

Thanks. I'll try work them out.

Regards
Terry

On Wed, Jul 1, 2015 at 7:29 PM, Erik Marklund <erik.marklund at chem.ox.ac.uk>
wrote:

> 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,
> Erik
>
> > 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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