Atila,
I use PYMOL to bring the PDB up, assign bond orders and then have it add
hydrogens. Write out the pdb file and then use antechamber to create the
mol2 file.
With the death of Warren DeLano I'm afraid that PYMOL has gone behind a
Schrodinger paywall. You may be able to find an older binary on the net.
Or I believe Schrodinger makes the source code available. I find it quite a
useful program.
Nic out
On 09/17/2015 11:44 AM, Atila Petrosian wrote:
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 - 11:00:06 PDT
