Yep, generally I remove all hydrogen before using leap...just logically it's a bit controversial that leap can't process files produced by Amber without any modifications.
Sincerely yours,
Andrew
09.06.10, 21:27, "Bill Ross" <ross.cgl.ucsf.EDU>:
> > I am trying to execute MM-PBSA tutorial on protein and small ligand for
> > which the PDB file was created by extraction of coordinates from the
> > trajectory file. These coordinates can be seen below. But I have problem in
> > saving the parameter and coordinates files. I can't understand why, because
> > I ve jsut used the file which was generated by Amber.
> >
> > FATAL: Atom .R.A does not have a type.
> > FATAL: Atom .R.A does not have a type.
> > Failed to generate parameters
> > Parameter file was not saved.
>
> Your GLU was probably in the middle of a strand (non-terminal).
> Loading it by itself, it is assumed to be NGLU, i.e. N-terminal.
> Delete the H's from pdb before loadpdb should solve it, provided
> you're happy with NGLU.
>
> Bill
>
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Received on Thu Jun 10 2010 - 06:00:03 PDT
