Hi! Just use openbabel to add the hydrogens.
obabel -h -ipdb lig.pdb -opdb > lig_h.pdb
will add hydrogens to make the molecule neutral
obabel -p 7.4 -ipdb lig.pdb -opdb > lig_p.pdb
will protonate the molecule to pH 7.4.
However, for your particular case it was not protonating the
pyridazinone nitrogen, given its pKa of 10.5 (according to the following
source).
https://books.google.com.ar/books?id=iUmBQSZTY3gC&pg=PA119&lpg=PA119&dq=pyridazinone+pka&source=bl&ots=QnOubU1QV7&sig=abJIQYQR9srjHYD4Ctp4FlGaYHg&hl=en&sa=X&ved=0ahUKEwi0grmUouXSAhVEH5AKHVX6CsAQ6AEIKDAA
So I've added the hydrogen manually using Avogadro to the lig_p.pdb
structure.
Knowing the right protonation state of a compound is not easy so the
above is just a quick guess. I suggest checking this more carefully.
Hope this helps!
Bruno
On 20/03/17 09:06, David Case wrote:
> On Mon, Mar 20, 2017, Nirupma Singh wrote:
>
>> I am trying to add hydrogens to my ligand file using reduce command in
>> amber but it is not adding any hydrogen to the ligand.
>> Database of HETATM connections:
>> "/opt/apps/amber14/dat/reduce_wwPDB_het_dict.txt"
> Reduce only knows about the ligands that are present in its database
> (above), which covers those ligands in the PDB repository. It is not a
> general-purpose program that can deal with arbitrary ligands, and it doens't
> know what to do with your molecule named "lig".
>
> You will need to either figure out what the PDB-standard name is for your
> ligand, and use other software, not present in AmberTools.
>
> ...good luck...dac
>
>
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Received on Mon Mar 20 2017 - 07:30:03 PDT
