> 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<NGLU 1>.A<H 18> does not have a type.
> FATAL: Atom .R<NGLU 123>.A<H 18> 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 Wed Jun 09 2010 - 10:30:06 PDT
