[AMBER] problem with reduce and energy minimization

From: Maryam Hamzehee <maryam_h_7860.yahoo.com>
Date: Thu, 21 Jan 2016 07:55:38 +0000 (UTC)

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
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