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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Received on Mon Nov 05 2012 - 10:30:03 PST
