very insightful message!
I will think about it!
Thank you!
On Tue, Aug 14, 2018 at 10:48 PM, Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> 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".]
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 14 2018 - 15:00:03 PDT
