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
>
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Received on Mon Sep 05 2022 - 01:00:02 PDT
