PS GLU is terminal, this is dimer, in each case this GLU ressidue is N terminal, but maybe I need to add manually NGLU, but agains it's strange why ambpdb doesn't do it in a way that leap can read then and save parameters.
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 - 06:30:05 PDT
