amazing reply! thank you!
[ to resolve, since I was not able to identify which amino-acid gives me
error, I delete all the hydogens and then they were successfully added
later on from tleap! ]
On Tue, Aug 14, 2018 at 4:33 PM, David A Case <david.case.rutgers.edu>
wrote:
> 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 - 11:30:02 PDT
