On Tue, Aug 14, 2018, Antonio Amber Carlesso wrote:
> *example_2*
> > mol=loadPDB tetramer_model_2_prepared_amber.pdb
> Loading PDB file: ./tetramer_model_2_prepared_amber.pdb
> Matching PDB residue names to LEaP variables.
> total atoms in file: 26034
> *Leap added 2 missing atoms according to residue templates:*
> * 2 H / lone pairs*
This is an information message only, and has been there for decades, so
we would not wish to change it. If it interferes with your workflow,
you would have to modify the code to remove it.
>
> *example_3*
> > mol=loadPDB tetramer_model_73_prepared_Amber_ok.pdb
> Loading PDB file: ./tetramer_model_73_prepared_Amber_ok.pdb
> Matching PDB residue names to LEaP variables.
> *Created a new atom named: HE2 within residue: .R<GLU 613>*
> *Created a new atom named: HE2 within residue: .R<GLU 1421>*
This is an error message, and cannot be ignored: it means that your pdb
files has "HE2" atoms (which probably mean the these glutamatic acids
are neutral), but residue "GLU" implies that they are deprotonated.
You would need to edit the PDB file, probably to change GLU to GLH.
(It's also possible to decide that the best fix is to delete the HE2
atoms....it's up to you. LEaP doesn't try to figure out what you really
want -- it just informs you that the atom names and residue names in the
input pdb file are not consistent.)
....hope this helps....dac
[Scott: maybe we should log the message in example_3 as in "error".]
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Received on Tue Aug 14 2018 - 08:00:03 PDT
