this is related to the forcefield you are using. I think there are a few
other posts on the list where you can find the exact solution, but
basically, for ff10 and ff12, you also need to load another file that tells
it about ions for your water model.
perhaps it's also in the manual, not sure.
On Mon, Nov 5, 2012 at 1:23 PM, David Condon <dec986.gmail.com> wrote:
> Hello everyone,
>
> I am attempting to load a PDB into tleap of an RNA tetramer.
>
> source leaprc.ff10
> > mol = loadpdb rna.pdb
> > addions mol Na+ 0
> > solvateoct mol TIP3PBOX 8.65
> > saveAmberParm mol prmtop inpcrd
> > quit
> >
>
> However, this does not recognize Na+:
>
> Mass > 22319.552 amu, Density > 0.828 g/cc
> > (type - hence mass - of one or more atoms could not be found)
> > Added 1172 residues.
> > Checking Unit.
> > Building topology.
> > Building atom parameters.
> > For atom: .R<Na+ 5>.A<Na+ 1> Could not find type: Na+
> > For atom: .R<Na+ 6>.A<Na+ 1> Could not find type: Na+
> > For atom: .R<Na+ 7>.A<Na+ 1> Could not find type: Na+
> > Parameter file was not saved.
> > Quit
> >
>
> and I don't know why. I've used leap files like this many times before and
> never had an issue with recognizing ions. I've also tried switching the
> addions/solvateoct lines but this gives the same error.
>
> any help is greatly appreciated,
> -Dave
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Mon Nov 05 2012 - 11:00:02 PST
