Did you load the ion libraries (generally right after sourcing the
leaprc.ff10)?
Ilyas Yildirim, Ph.D.
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On Mon, 5 Nov 2012, David Condon 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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Received on Mon Nov 05 2012 - 11:00:02 PST
