Dear All,
I am have been trying to dock the in-bound ligand of PDB 1m52, back to protein as according to the recommended protocol (http://www.nmr.sinica.edu.tw/Course/Course20080311/doc/DS20_2Dock(ligandfit).pdf)
but I cant. Anyone can help?
Procedure I did :
1) 'Clean' the crystal structure
2) "Structure\Remove Cell
3) Remove water
4) Cut out the in-bound ligand, paste to another 3D windows (Molecule)
5) Apply forcefield "CHARMm" on Protein - A & B ; "CHARMm on Molecule"
6) Select Protein A and B as Receptor "Tool\Binding Site\Define Selected Residue as Receptor"
7) Find binding Site from receptor cavities
8) Protocol \ Docking (LigandFit) - Input Receptor : 1m52 ; Input Ligand : Molecule ; Binding Site : SIte 1
9)
a) Output : Zero pose
b) Log file :
Run started at: Sun Nov 13 16:20:17 2011 on: PC win32
Read docking and energy parameter file: LF_param.txt
Read site data file: BindingSite.txt
Site partition: 1 site partition(s) produced
Site partition(s) from site data file: 1
Prepare dreiding grid, size: 53 75 48
Grid calculation finished in 78.5[s]
Monte Carlo Docking Parameters:
TORSION ITERATIONS STOP_STEPS
(1) 2 500 120
(2) 4 1200 300
(3) 6 1500 350
(4) 10 2000 500
(5) 25 3000 750
(6) 100 0 0
----------------------------------------
Molecule: Molecule-1
Molecule no. : 1
Rotatable bonds: 4
MC termination values: 4800 / 1200
Flexible Docking ... done 0.0[s]
docking message: no hit found
docking message: ligand's shape does not match any site.
----------------------------------------
Poses saved: 0
Ligands without hits: 1
Total elapsed time: 1:21 [min:sec]
Run completed at: Sun Nov 13 16:21:38 2011
Released license for ligfit_ext...
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may I know whether my protocol is correct or not? Why would i get no shape matching when this is a small molecule which is an in-bound ligand to the crystal strucuture ?
Appreciate your help ! =)
Thank you
Regards,
Mai
