Dear All
I am trying to do energy minimization of my ligand-protein complex. My ligand is small molecule. I followed the tutorial Antechamber tutorial (Simulating Sustiva (efavirenz)-RT complex). I did not manage to add hydrogens to the ligand (extracted from crystal structure). I used reduce command and got the following error:
reduce: version 3.14 08/21/2008, Copyright 1997-2008, J. Michael WordProcessing file: "lzu_h_gold.pdb"Database of HETATM connections: "/share/apps/amber11//dat/reduce_wwPDB_het_dict.txt"Processing only 'A' conformations.VDW dot density = 16/A^2Orientation 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| < 0.66Aromatic rings in amino acids accept hydrogen bonds.Building or keeping OH & SH Hydrogens.Rotating NH3 Hydrogens.Processing Met methyls.*WARNING*: Res "LZU" not in HETATM Connection Database. Hydrogens not added.Found 26 hydrogens (26 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
I added hydrogens to the ligand through GOLD software and removed the connections from the corresponding file. I continued the procedure without using reduce command, and produced the *.frcmod and *.lib files. But when I was trying to do energy minimization via sander command it stopped suddenly :
Here are the min.in and mdinfo files
Initial minimisation of AO-lzu complex &cntrl imin=1, maxcyc=500, ncyc=50, cut=16, ntb=0, igb=1, &end
mdinfo: NSTEP ENERGY RMS GMAX NAME NUMBER 71 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = NaN DIHED = NaN VDWAALS = 0.0000 EEL = 0.0000 EGB = -265619.6596 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
additionally, I did energy minimization for the protein (without ligand), there was not any problem and I think there is something wrong with ligand. I was wondering if there is a general ligand name or I should edit and add the connectivity information to the reduce_wwPDB_het_dict.txt file. What can I do in this regard.The files are attached.
Your help in this regard would be highly appreciated.
Best regardsMaryam
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Received on Thu Jan 21 2016 - 00:00:03 PST
