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 - 09:00:05 PDT
