P.S. well I could find a temporal solution adding missed hydrogens to
the ligand using pymol which should not be an ideal algorithm. However
it does not produce any artifacts and the systems are perfectly
parametrized using antechamber etc.
Anyway it would be great to have some utility (e.g. built in
amber-tools) to do such conversion directly via the terminal...
Il giorno lun 5 set 2022 alle ore 09:43 Enrico Martinez
<jmsstarlight.gmail.com> ha scritto:
>
> great, thank you Valentin!
> Are there others solutions that could be integrated into the pipeline
> without GUI ?
> Cheers
> Enrico
>
> Il giorno ven 2 set 2022 alle ore 19:18 Rybenkov, Valentin V.
> <valya.ou.edu> ha scritto:
> >
> > Hello Enrico,
> >
> >
> >
> > Yes, OpenBabel does that. I use chemdraw to prepare molecules (chem3D is friendlier for that). You can also use online tools to convert SMILES into SDF or mol.
> >
> >
> >
> > Valentin V. Rybenkov
> > University of Oklahoma
> > 101 Stephenson Parkway
> > Norman, OK 73019
> > Web: antibiotics.oucreate.com
> >
> >
> >
> > From: Enrico Martinez via AMBER
> > Sent: Friday, September 2, 2022 11:58 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] problem of the protonation of the ligand
> >
> >
> >
> > Dear Amber Users!
> > I've just noticed a bug related to the preparation of the ligand for
> > md simulation.
> > In fact, on the step of the adding hydrogens via babel,
> > obabel lig_withoutH.pdb -O lig_withH.pdb -h
> >
> > depending on the initial structure of the ligand, sometimes some extra
> > hydrogens are added resulting in wrong geometry of the compound. After
> > that antechamber could not generate input parameters for such
> > compounds. Would it be possible to add hydrogens to the ligand in
> > another way to avoid such issue or alternatively to use some option
> > for open-babel to check the output ?
> > Many thanks in advance
> > Cheers
> > Enrico
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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Received on Mon Sep 05 2022 - 03:00:02 PDT
