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
>>>
>>>
>>
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Received on Tue Sep 06 2022 - 09:30:02 PDT
