Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type.

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Wed, 9 Jun 2010 10:27:10 -0700

> 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.


AMBER mailing list
Received on Wed Jun 09 2010 - 10:30:06 PDT
Custom Search