Dear Amber users
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. I am getting the
following error :
reduce ligand.pdb>ligah.pdb
reduce: version 3.24 07/24/2013, Copyright 1997-2013, J. Michael Word
Processing file: "ligand.pdb"
Database of HETATM connections:
"/opt/apps/amber14/dat/reduce_wwPDB_het_dict.txt"
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.
Found 0 hydrogens (0 hets)
Standardized 0 hydrogens (0 hets)
Added 0 hydrogens (0 hets)
Removed 0 hydrogens (0 hets)
If you publish work which uses reduce, please cite:
Word, et. al. (1999) J. Mol. Biol. 285, 1735-1747.
For more information see
http://kinemage.biochem.duke.edu
Please help me resolving the issue. I have also attached the ligand file.
--
Regards
Nirupma Singh
PhD Scholar
Netaji Subhas Institute of Technology
Dwarka, Delhi
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Received on Sun Mar 19 2017 - 23:00:02 PDT
