Hey Sergio,
Thank you for your reply!
yep actually the problem is in the aromatic system containing 2 NH and
2 C=O(H) so either it should be protonated in H, or in C=0H depending
on the aromaticity of the whole ring. I could do it via VMD but
chimera-X did not protonate the N-H.
Cheers,
Enrico
Il giorno mar 6 set 2022 alle ore 18:01 sribone via AMBER
<amber.ambermd.org> ha scritto:
>
> Chimera is one of the best to add H to a ligand, it almoust never
> fails... What kind of ligand are you using? Probably your problem is
> coming from the atom types in your ligand...
>
> Regards.
>
> Sergio
>
> On 6/9/22 12:50, Rybenkov, Valentin V. via AMBER wrote:
> > Chemaxon used to be free for academics with minor strings attached
> >
> > Valentin V. Rybenkov
> > University of Oklahoma
> > 101 Stephenson Parkway
> > Norman, OK 73019
> > Web: antibiotics.oucreate.com
> >
> > From: Enrico Martinez<mailto:jmsstarlight.gmail.com>
> > Sent: Tuesday, September 6, 2022 10:46 AM
> > To: Rybenkov, Valentin V.<mailto:valya.ou.edu>
> > Cc: AMBER Mailing List<mailto:amber.ambermd.org>
> > Subject: Re: [AMBER] problem of the protonation of the ligand
> >
> > 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
>
> _______________________________________________
> 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 - 09:30:03 PDT
