Reduce will only compare to a database (as it says in the output). This will require the residue name to be set properly, assuming that your molecule is indeed in the dictionary.
There are various software packages that will add hydrogen e.g. avogadro or chimera to name just a few. Any chemical drawing program should be able to do that. But all those programs typically do is just valence filling. Eventually, it's a matter of understanding the chemistry.
________________________________________
From: Atila Petrosian [atila.petrosian.gmail.com]
Sent: 17 September 2015 16:44
To: david.case.rutgers.edu; AMBER Mailing List
Subject: Re: [AMBER] antechamber error
Dear David,
Thanks for your answer.
Before using antechamber, I used following commnad:
$AMBERHOME/exe/reduce lig.pdb > lig_h.pdb
reduce: version 3.14 08/21/2008, Copyright 1997-2008, J. Michael Word
Processing file: "lig.pdb"
Database of HETATM connections:
"/home/linux/Desktop/amber/amber11/dat/reduce_wwPDB_het_dict.txt"
Processing only 'A' conformations.
VDW dot density = 16/A^2
Orientation penalty scale = 1 (100%)
Eliminate contacts within 3 bonds.
Ignore atoms with |occupancy| <= 0.01 during adjustments.
Waters ignored if B-Factor >= 40 or |occupancy| < 0.66
Aromatic rings in amino acids accept hydrogen bonds.
Building or keeping OH & SH Hydrogens.
Rotating NH3 Hydrogens.
Processing Met methyls.
WARNING: atom H171 from LIG will be treated as hydrogen
WARNING: atom H171 from LIG will be treated as hydrogen
WARNING: atom H172 from LIG will be treated as hydrogen
WARNING: atom H172 from LIG will be treated as hydrogen
WARNING: atom H171 from LIG will be treated as hydrogen
WARNING: atom H172 from LIG will be treated as hydrogen
WARNING: atom HC10 from LIG will be treated as hydrogen
WARNING: atom HC10 from LIG will be treated as hydrogen
WARNING: atom HC13 from LIG will be treated as hydrogen
WARNING: atom HC13 from LIG will be treated as hydrogen
WARNING: atom HC15 from LIG will be treated as hydrogen
WARNING: atom HC15 from LIG will be treated as hydrogen
WARNING: atom HC22 from LIG will be treated as hydrogen
WARNING: atom HC22 from LIG will be treated as hydrogen
WARNING: atom HC24 from LIG will be treated as hydrogen
WARNING: atom HC24 from LIG will be treated as hydrogen
WARNING: atom HC26 from LIG will be treated as hydrogen
WARNING: atom HC26 from LIG will be treated as hydrogen
WARNING: atom HC28 from LIG will be treated as hydrogen
WARNING: atom HC28 from LIG will be treated as hydrogen
Found 2 hydrogens (2 hets)
Standardized 0 hydrogens (0 hets)
Added 0 hydrogens (0 hets)
Removed 0 hydrogens (0 hets)
Unfortunately, no H atom was added in lig_h.pdb file.
Is ther another way to addidng H atoms to my ligand?
Best,
Atila
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Received on Thu Sep 17 2015 - 10:30:03 PDT
