Hi,
The reduce_wwPDB_het_dict.txt is where it should be. I think the AMBERHOME variable is set correctly since all the others steps perform fine. I have attached the output pdb. The output in the terminal is as follows:
Processing file: "sustiva.pdb"
Database of HETATM connections: "/home/mikhail/Downloads/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.
SKIPPED H( A 999 SUS HO1 ): A 999 SUS O1 bonds- A 999 SUS C14 (short bond)
SKIPPED H( A 999 SUS H2 ): A 999 SUS C2 bonds- A 999 SUS C3 (H bumps)
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
Thank you.
________________________________
From: Ziheng Wang
Sent: Saturday, April 4, 2015 3:34 PM
To: amber.ambermd.org
Subject: Question Regarding reduce function of Antechamber
Dear all,
I have been following tutorial B4, the protein-ligand system with sustiva. I tried to reduce the sustiva pdb file by using reduce sustiva > sustiva_h.pdb. However, the terminal log and the produced sustiva_h.pdb show that no hydrogens are added, as a result, the new sustiva_h.pdb has an odd number of electrons and cannot be processed by sqm. I wonder what caused the problem with the reduce method and how to fix it.
Thank you,
Tony
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Received on Sun Apr 05 2015 - 12:30:02 PDT
