Hi,
I am trying to use reduce to add hydrogens to one protein-ligand complex.
However, it is not adding the hydrogens to the ligand (while it is working
for the protein). Even if I try to run on the ligand alone I cannot get any
added hydrogen (despite no errors are displayed); this is my ligand
HETATM 1 O LIG 1 28.803 34.412 24.810
HETATM 2 O LIG 1 32.348 34.820 22.811
HETATM 3 C LIG 1 31.184 34.930 24.864
HETATM 4 C LIG 1 28.888 34.181 23.441
HETATM 5 C LIG 1 29.942 34.776 25.486
HETATM 6 C LIG 1 30.033 34.309 22.756
HETATM 7 C LIG 1 31.292 34.697 23.412
HETATM 8 C LIG 1 32.304 35.302 25.610
HETATM 9 C LIG 1 29.819 34.994 26.858
HETATM 10 C LIG 1 32.177 35.519 26.983
HETATM 11 C LIG 1 30.938 35.365 27.605
HETATM 12 C LIG 1 27.590 33.799 22.863
HETATM 13 C LIG 1 27.535 32.853 21.841
HETATM 14 C LIG 1 26.305 32.489 21.295
HETATM 15 C LIG 1 25.130 33.072 21.771
HETATM 16 C LIG 1 25.186 34.019 22.794
HETATM 17 C LIG 1 26.417 34.383 23.341
HETATM 18 N LIG 1 23.877 32.701 21.214
HETATM 19 O LIG 1 23.820 32.389 20.000
HETATM 20 O LIG 1 22.862 32.695 21.951
HETATM 21 N LIG 1 30.041 34.083 21.352
HETATM 22 O LIG 1 30.530 33.017 20.951
HETATM 23 O LIG 1 29.559 34.969 20.632
HETATM 24 N LIG 1 33.311 35.898 27.749
HETATM 25 O LIG 1 34.058 35.003 28.212
HETATM 26 O LIG 1 33.534 37.117 27.941
TER
END
and this is what I get from reduce (Amber14)
reduce: version 3.24 07/24/2013, Copyright 1997-2013, J. Michael Word
Processing file: "lig.pdb"
Database of HETATM connections:
"/home/fgentile/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.
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
WARNING: atom HC28 from LIG will be treated as hydrogen
WARNING: atom HC28 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 HC24 from LIG will be treated as hydrogen
WARNING: atom HC24 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 HC15 from LIG will be treated as hydrogen
WARNING: atom HC15 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 HC10 from LIG will be treated as hydrogen
WARNING: atom HC10 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 H171 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
Found 0 hydrogens (0 hets)
Standardized 0 hydrogens (0 hets)
Added 0 hydrogens (0 hets)
Removed 0 hydrogens (0 hets)
USER MOD reduce.3.24.130724 H: found=0, std=0, add=0, rem=0, adj=0
HETATM 1 O LIG 1 28.803 34.412 24.810 0.00 0.00
HETATM 2 O LIG 1 32.348 34.820 22.811 0.00 0.00
HETATM 3 C LIG 1 31.184 34.930 24.864 0.00 0.00
HETATM 4 C LIG 1 28.888 34.181 23.441 0.00 0.00
HETATM 5 C LIG 1 29.942 34.776 25.486 0.00 0.00
HETATM 6 C LIG 1 30.033 34.309 22.756 0.00 0.00
HETATM 7 C LIG 1 31.292 34.697 23.412 0.00 0.00
HETATM 8 C LIG 1 32.304 35.302 25.610 0.00 0.00
HETATM 9 C LIG 1 29.819 34.994 26.858 0.00 0.00
HETATM 10 C LIG 1 32.177 35.519 26.983 0.00 0.00
HETATM 11 C LIG 1 30.938 35.365 27.605 0.00 0.00
HETATM 12 C LIG 1 27.590 33.799 22.863 0.00 0.00
HETATM 13 C LIG 1 27.535 32.853 21.841 0.00 0.00
HETATM 14 C LIG 1 26.305 32.489 21.295 0.00 0.00
HETATM 15 C LIG 1 25.130 33.072 21.771 0.00 0.00
HETATM 16 C LIG 1 25.186 34.019 22.794 0.00 0.00
HETATM 17 C LIG 1 26.417 34.383 23.341 0.00 0.00
HETATM 18 N LIG 1 23.877 32.701 21.214 0.00 0.00
HETATM 19 O LIG 1 23.820 32.389 20.000 0.00 0.00
HETATM 20 O LIG 1 22.862 32.695 21.951 0.00 0.00
HETATM 21 N LIG 1 30.041 34.083 21.352 0.00 0.00
HETATM 22 O LIG 1 30.530 33.017 20.951 0.00 0.00
HETATM 23 O LIG 1 29.559 34.969 20.632 0.00 0.00
HETATM 24 N LIG 1 33.311 35.898 27.749 0.00 0.00
HETATM 25 O LIG 1 34.058 35.003 28.212 0.00 0.00
HETATM 26 O LIG 1 33.534 37.117 27.941 0.00 0.00
TER
END
the program is working properly with the sustiva molecule from the
tutorial...Any idea? Thanks in advance
--
Francesco Gentile
PhD Student, Biophysics
CCIS 3-215, Department of Physics
7-112, Li Ka Shing Centre for Health Research Innovation
University of Alberta, Edmonton, AB T6G 2E1
Canada
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Received on Thu Mar 19 2015 - 22:00:02 PDT
