On Fri, Mar 07, 2014, Baifan Wang wrote:
>
> It seems you are loading an RNA or a DNA molecule in leap. Before you load
> a pdb into leap, you should check the pdb file that the residues name of
> the pdb correspond to the regular name.
> For example, the residues name of A G T C of DNA in leap shoule be DA DG DT
> DC, and the residues name of A G U C of DNA in leap shoule be RA RG RU RC.
Note that this is not true, at least for current force fields (since about
2010): RNA residues follow the PDB standard: A G U C. (*not* RA, etc.)
> > I met a problem in using xleap. I load the rna pdb file, and try to save
> > the prmtop and inpcrd file. But I can't save it and it shows the following
> > error message:
> > FATAL: Atom .R<A36 504>.A<P 1> does not have a type.
> > FATAL: Atom .R<A36 504>.A<O1P 2> does not have a type.
> > FATAL: Atom .R<A36 504>.A<O2P 3> does not have a type.
> > FATAL: Atom .R<A36 504>.A<O5' 4> does not have a type.
> > FATAL: Atom .R<A36 504>.A<C5' 5> does not have a type.
> > FATAL: Atom .R<A36 504>.A<C4' 6> does not have a type.
We can't help without knowing where you got your pdb file, and what commands
you gave to LEaP. Look at PDB files from www.rcsb.org, and try to use the
same atom and residue names. It looks(?) like your PDB file may have residue
names like "A36"; if so, those will need to be changed to standard names.
...dac
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Received on Fri Mar 07 2014 - 06:00:03 PST
