Dear Antonio,
Just to add on this comment...
> [ 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! ]
Notice that leap informs you the exact residue numbers in the warning message:
> *Created a new atom named: HE2 within residue: .R<GLU 613>*
> *Created a new atom named: HE2 within residue: .R<GLU 1421>*
In this case 613 and 1421... the numeration corresponds to the residue indexes in the topology (starting from 1), which may differ from the biological (PDB) sequence.
You can get the PDB/AMBER equivalence by using the following command:
pdb4amber -i yourPDB.pdb
And then looking at file "stdout_renum.txt" (first two columns correspond to PDB, second two to AMBER topology)
I'm pointing this because of David's important comment:
> ...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...
I certainly don't know about your system, but "solving" an error message doesn't mean solving a system issue... (e.g. a charged residue inside a hydrophobic pocket may be dramatic for the protein structure)
You may find some other hints by reading all threads from this mail [
http://archive.ambermd.org/201807/0149.html]
Best,
MatÃas
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/laboratorios-eng/lsbm]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Antonio Amber Carlesso" <antonio.amber.carlesso.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Martes, 14 de Agosto 2018 15:20:17
Asunto: Re: [AMBER] tleap_protein_preparation_general_rule
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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>
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Received on Tue Aug 14 2018 - 14:00:01 PDT
