Hey Valentin,
Actually I've already tried add protons to the ligand using
reduce, pymol, chimerax, vmd, openbabel
:-)
I've never heard about ChemAxon, is it free software ??
Many thanks in advance!
Cheers
Enrico
Il giorno mar 6 set 2022 alle ore 16:52 Rybenkov, Valentin V.
<valya.ou.edu> ha scritto:
>
> Hi Enrico,
>
>
>
> I am not into high-throughput calculations. Did you try AmberTools or ChemAxon? They work off command line.
>
>
>
> Valentin V. Rybenkov
> University of Oklahoma
> 101 Stephenson Parkway
> Norman, OK 73019
> Web: antibiotics.oucreate.com
>
>
>
> From: Enrico Martinez
> Sent: Monday, September 5, 2022 2:44 AM
> To: Rybenkov, Valentin V.
> Cc: AMBER Mailing List
> Subject: Re: [AMBER] problem of the protonation of the ligand
>
>
>
> 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
> >
> >
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 06 2022 - 09:00:02 PDT
