MolDyn

Docking of Ligand on Protein


NOTE!!
To perform docking of Ligand on Protein, one need
1) PDB file prot_Lig_Complex.pdb. The file define protein structure and Ligand initial structure.
   Ligand can be near from protein surface, i.e. in contact in abbitrary position and orientation.
2) The Ligand molecular topology should be described in
   ~/dat/bs_lig_all94.dat file 
   according to general rule, see examples for TEST#1 - TEST#8
   It includes CONNECTIVITY, ATOM NAMES =(equivalent to PDB), ATOM ForcrField CODE according to AMBER94 FF,
   ATOMIC CHARGES.
   PROCEDURE to automatically generate LIG_TOPO file from LIG.pdb  file in PREPARATION.
The bs_lig_all94.dat  file includes topology data for 12 Ligands.

!Note, that Ligands of peptide nature (i.e. short peptides) or oligonucleotides DO NOT NEED any topology data,
These LIGANDS will use the PREEXISTED topology for PRotein RESidues and NUcleic acid RESidues.

*************************************************************************************************

Directory ./tLg shows examples of Ligand Docking on peptides:
#
# DOCK TEST#1
./1bty - trypsine-benzamidine complex
1bty.ben.Native.pdb - protein-lig complex with NATIVE binding mode for Ligand
1bty.ben.notNative.pdb - protein-lig complex with notNATIVE (arbitryry) mode for Ligand 
the both files can be used as inPDB file

#
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 1bty.P.pdb -cL ben.notNative.pdb -i MdynPar_1bty.inp -sa SAprotocol_long.inp -mn 1bty -o 1bty.out
#
UNDESTANDING DOCKING RESULTS:

1) file 1bty.bSiteAtOnSAS00.pdb shows positions of binding site candidates 
   on the protein surface
 #LigBindGridOnSAS:
 ATOM      1  LBSt        1      16.536  26.130   8.764   11
 ATOM      2  LBSt        2      29.319  14.972  16.378   11
 ATOM      3  LBSt        3       6.595  15.454  32.366    9
 ATOM      4  LBSt        4      28.049  26.396   3.572    9
 ATOM      5  LBSt        5      37.370  14.662  29.278    8
 ATOM      6  LBSt        6       9.605  28.662  39.481    7
 ATOM      7  LBSt        7      18.280  35.574  15.402    7
 ATOM      8  LBSt        8      30.648  34.679  44.060    7
 ATOM      9  LBSt        9      34.040  33.767  21.484    7
 ATOM     10  LBSt       10       5.056  19.922  18.987    6
 ATOM     11  LBSt       11      25.308   5.865  13.437    6
 ATOM     12  LBSt       12      13.241  31.812  30.019    6
  ...
  ATOM     40  LBSt       40      25.260   6.929  29.909    4
  ATOM     41  LBSt       41      26.781  13.047  43.008    4

Docking alhorithm put ligand center into this positions with SCore >= 6 
and refine ligand orientation and conformation
via semiglobal optimization by Simulated annealing coupled with protein-Ligand force field deformation.
#
The resulting ligand positions are collected in the files :
1bty.LigDockFin000.001.pdb
1bty.LigDockFin000.002.pdb
1bty.LigDockFin000.003.pdb
1bty.LigDockFin001.001.pdb
1bty.LigDockFin001.002.pdb
1bty.LigDockFin001.003.pdb
...
1bty.LigDockFin015.003.pdb
#
File 1bty.LigDockFin.ePL.res : 
collects the refined total Potential energy of internal Lig-Lig + Lig-Prot 
interactions for final Ligand Docking modes  from
files 1bty.LigDockFin*.pdb
#
NN   LigDockFinXXX.XXX.pdb      ePLtot  eVDW    eCoul   eHb     eSolv   eGeo    tempTAv
   1 ./LigDockFin001.001.pdb    -24.3   -11.6    -0.6    -9.4    -6.9     4.3    50.2
   2 ./LigDockFin001.002.pdb    -24.2   -11.0    -1.2    -9.8    -6.8     4.6    50.2
   3 ./LigDockFin001.003.pdb    -24.0   -10.7    -1.3    -9.6    -6.9     4.5    50.2
   4 ./LigDockFin002.001.pdb    -39.3   -20.7    -6.2   -11.0    -4.5     3.1    51.8  - best RMSD mode
   5 ./LigDockFin002.002.pdb    -39.3   -20.6    -6.1   -12.8    -4.5     4.8    51.8
   6 ./LigDockFin002.003.pdb    -39.1   -20.7    -7.0   -10.3    -4.5     3.4    51.8
   7 ./LigDockFin003.001.pdb    -18.6    -1.2    -2.5    -9.4    -6.8     1.3    46.5
   8 ./LigDockFin003.002.pdb    -17.7    -2.4    -1.6    -9.6    -6.5     2.5    46.5
   9 ./LigDockFin003.003.pdb    -17.7    -2.1    -2.7    -9.7    -6.7     3.6    46.5
  10 ./LigDockFin004.001.pdb    -27.8    -4.5    -7.6    -9.9    -7.5     1.7    51.0
  11 ./LigDockFin004.002.pdb    -27.7    -5.6    -7.5    -9.6    -7.4     2.4    51.0
  12 ./LigDockFin004.003.pdb    -27.7    -5.4    -7.3    -9.9    -7.4     2.3    51.0
  13 ./LigDockFin005.001.pdb    -30.1   -10.8    -5.6    -9.6    -6.3     2.2    48.5
  14 ./LigDockFin005.002.pdb    -29.8   -11.6    -5.2    -9.5    -6.3     2.8    48.5
  15 ./LigDockFin005.003.pdb    -29.6   -12.4    -4.5    -9.5    -6.3     3.1    48.5
  16 ./LigDockFin006.001.pdb    -22.7    -9.0    -1.5    -9.5    -6.3     3.5    50.4
  17 ./LigDockFin006.002.pdb    -22.5    -8.6    -1.6    -9.4    -6.4     3.5    50.4
  18 ./LigDockFin006.003.pdb    -22.5    -7.9    -2.1    -9.3    -6.1     3.0    50.4
#
****************************************************************
#

# DOCK TEST#2
alpha-thrombin/bemzamidine complex : 1dwb
#
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 1dwb.P.pdb -cL ben.notNative.pdb -i MdynPar_1dwb.inp -sa SAprotocol_long.inp -mn 1dwb -o
 1dwb.out 
#
file 1dwb.LigDockFin.ePL.res: - total potential energy of Lig-Lig + Lig-Prot interactions:
#
NN   LigDockFinXXX.XXX.pdb      ePLtot  eVDW    eCoul   eHb     eSolv   eGeo    tempTAv
   1 1dwb.LigDockFin001.001.    -43.7   -16.6   -11.6   -13.9    -5.5     3.9    47.4   - best docking mode
   2 1dwb.LigDockFin001.002.    -43.3   -16.5   -11.0   -14.3    -5.5     4.0    47.4   -best docking mode
   3 1dwb.LigDockFin001.003.    -43.3   -17.1   -10.7   -14.1    -5.5     4.1    47.4   - best docking mode
   4 1dwb.LigDockFin002.001.    -25.2    -8.2    -2.9    -9.7    -7.7     3.4    48.4
   5 1dwb.LigDockFin002.002.    -24.9    -8.3    -3.4    -9.6    -7.7     4.0    48.4
   6 1dwb.LigDockFin002.003.    -24.6    -7.4    -3.4    -9.8    -7.6     3.6    48.4
   7 1dwb.LigDockFin003.001.    -31.6   -10.7    -6.1   -10.9    -7.1     3.2    50.1
   8 1dwb.LigDockFin003.002.    -31.2    -9.9    -6.3   -11.1    -6.9     2.9    50.1
   9 1dwb.LigDockFin003.003.    -31.2   -11.1    -5.8   -10.4    -7.0     3.1    50.1
  10 1dwb.LigDockFin004.001.    -20.2    -9.0    -2.1    -7.9    -5.6     4.4    50.4
  11 1dwb.LigDockFin004.002.    -19.7    -8.3    -2.2    -8.1    -5.7     4.5    50.4
  12 1dwb.LigDockFin004.003.    -19.4    -9.0    -2.3    -8.0    -5.7     5.5    50.4
  13 1dwb.LigDockFin005.001.    -29.9    -4.5    -9.4    -9.9    -8.3     2.2    52.1
  14 1dwb.LigDockFin005.002.    -29.9    -8.9   -10.7   -11.8    -9.0    10.5    52.1
  15 1dwb.LigDockFin005.003.    -29.8   -10.7    -6.4    -7.1    -9.0     3.4    52.1
  16 1dwb.LigDockFin006.001.    -21.9    -5.9    -2.0    -9.4    -7.3     2.7    51.3
  17 1dwb.LigDockFin006.002.    -21.8    -7.3    -1.7    -9.1    -7.2     3.5    51.3
  18 1dwb.LigDockFin006.003.    -21.7    -6.3    -2.4    -9.5    -7.2     3.6    51.3
  19 1dwb.LigDockFin007.001.    -23.7    -8.4    -1.2    -9.5    -7.8     3.2    49.4
  20 1dwb.LigDockFin007.002.    -23.6    -8.2    -1.8    -9.2    -7.8     3.3    49.4
  21 1dwb.LigDockFin007.003.    -23.1    -7.9    -2.1    -9.5    -7.6     4.0    49.4
..

***************************************************************************************
#DOCK TEST#3
./1dwc    - alpha-Thrombin/MIT ligand complex
#
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 1dwc.P.pdb -cL 1dwc.Lig.pdb -i MdynPar_d21.inp -sa SAprotocol_long.inp -mn 1dwc -o
 1dwc.out
#
Docking result potential energy file:
1dwc.ePL.LigDockFin.res:
#
NN   LigDockFinXXX.XXX.pdb      ePLtot  eVDW    eCoul   eHb     eSolv   eGeo    tempTAv
   1 1dwc.LigDockFin001.001.    -64.5   -45.0   -14.3   -20.9   -17.5    33.3    49.7 - best eP_mode
   2 1dwc.LigDockFin001.002.    -61.2   -42.9   -16.0   -22.3   -14.7    34.7    49.7 - best rmsd_mode
   3 1dwc.LigDockFin001.003.    -52.8   -33.9   -15.4   -22.3   -24.3    43.0    49.7
   4 1dwc.LigDockFin002.001.    -53.7   -35.1   -10.4   -24.2   -23.2    39.3    50.7
   5 1dwc.LigDockFin002.002.    -49.9   -30.1   -16.1   -21.7   -23.6    41.7    50.7
   6 1dwc.LigDockFin002.003.    -44.6   -29.8   -10.3   -22.1   -21.5    39.1    50.7
   7 1dwc.LigDockFin003.001.    338.3   194.2     5.7    -4.2   -13.8   156.4    53.1
   8 1dwc.LigDockFin003.002.    340.4   230.8   -12.9   -19.3   -15.6   157.4    53.1
   9 1dwc.LigDockFin003.003.    368.8   224.5    -2.5   -10.8   -13.3   170.9    53.1
  10 1dwc.LigDockFin004.001.    -49.8   -34.1   -13.2   -24.9   -14.4    36.8    50.5
  11 1dwc.LigDockFin004.002.    -48.6   -26.5   -13.2   -27.2   -14.5    32.8    50.5
  12 1dwc.LigDockFin004.003.    -47.2   -27.0   -16.5   -27.6   -12.1    36.1    50.5
  13 1dwc.LigDockFin005.001.    165.1    81.5    -2.2   -13.8   -19.8   119.4    52.8
  14 1dwc.LigDockFin005.002.    290.1   183.9    -8.2   -13.1   -11.4   138.8    52.8
  15 1dwc.LigDockFin005.003.    303.4   147.8     2.2    -8.3   -17.0   178.7    52.8
  16 1dwc.LigDockFin006.001.    -58.5   -37.5   -15.3   -18.4   -25.9    38.6    47.6
  17 1dwc.LigDockFin006.002.    -58.4   -37.1   -17.6   -25.7   -21.6    43.6    47.6
  18 1dwc.LigDockFin006.003.    -57.2   -30.6   -16.8   -18.6   -26.7    35.6    47.6
  19 1dwc.LigDockFin007.001.    -58.9   -26.3   -26.3   -29.3   -19.0    42.0    49.0
  20 1dwc.LigDockFin007.002.    -57.6   -26.6   -21.5   -24.0   -20.4    35.0    49.0
  21 1dwc.LigDockFin007.003.    -57.3   -28.2   -21.7   -24.5   -19.3    36.3    49.0
...
****************************************************************************************
#
DOCK TEST#4
./1stp : complex streptavidine/biotin
#
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 1stp.P.pdb -cL 1stp.btn.Lig.pdb -i MdynPar_d21.inp -sa SAprotocol_long.inp -mn 1stp -o
 1stp.out
Docking result potential energy file:
1stp.LigDockFin.ePL.res
#
NN   LigDockFinXXX.XXX.pdb      ePLtot  eVDW    eCoul   eHb     eSolv   eGeo    tempTAv
   1 1stp.LigDockFin001.001.    -56.1   -35.0   -12.9   -25.5    -8.0    25.4    49.4 - best eP_mode/rmsd_mode
   2 1stp.LigDockFin001.002.    -55.7   -34.5   -13.4   -25.3    -7.7    25.2    49.4
   3 1stp.LigDockFin001.003.    -55.7   -33.8   -13.9   -25.6    -7.8    25.4    49.4
   4 1stp.LigDockFin002.001.    -19.5   -21.3    -5.0    -8.6   -10.3    25.7    50.8
   5 1stp.LigDockFin002.002.    -18.5   -26.3    -4.6    -8.6    -7.5    28.5    50.8
   6 1stp.LigDockFin002.003.    -17.5   -20.7    -6.5    -9.5   -11.0    30.3    50.8
   7 1stp.LigDockFin003.001.    -19.9   -16.5    -9.4   -14.4   -10.2    30.6    50.6
   8 1stp.LigDockFin003.002.    -19.7   -19.5   -10.2   -14.6    -5.8    30.3    50.6
   9 1stp.LigDockFin003.003.    -19.3   -19.1    -8.5   -13.8    -6.3    28.5    50.6
  10 1stp.LigDockFin004.001.    -11.7   -12.3    -6.4    -9.5    -9.3    25.8    51.0
  11 1stp.LigDockFin004.002.    -11.6   -14.5    -4.3    -9.8   -10.2    27.2    51.0
  12 1stp.LigDockFin004.003.    -10.3   -12.8    -5.5    -9.6    -8.9    26.5    51.0
  13 1stp.LigDockFin005.001.    -12.9   -14.9    -7.7    -9.8    -6.9    26.3    51.1
  14 1stp.LigDockFin005.002.    -12.8   -16.8    -5.1    -4.9   -11.0    25.2    51.1
  15 1stp.LigDockFin005.003.    -11.0   -13.1    -9.3    -8.7    -7.2    27.3    51.1
  16 1stp.LigDockFin006.001.    -26.2   -17.1   -15.3   -18.3    -2.5    27.1    49.4
  17 1stp.LigDockFin006.002.    -26.2   -17.2   -15.4   -18.4    -2.6    27.3    49.4
  18 1stp.LigDockFin006.003.    -23.0   -17.9   -13.3   -14.9    -3.9    26.9    49.4
  19 1stp.LigDockFin007.001.    -30.4   -16.2   -17.2   -27.9     0.2    30.8    47.0
  20 1stp.LigDockFin007.002.    -29.2   -12.6   -18.3   -28.0     1.3    28.4    47.0
  21 1stp.LigDockFin007.003.    -28.1   -15.0   -18.5   -22.6    -0.2    28.2    47.0
..
NOTE!: three mode 1stp.LigDockFin001.001.pdb 
                  1stp.LigDockFin001.002.pdb
                  1stp.LigDockFin001.003.pdb
are found by MD SA optimization from different initial orientations of the ligand
****************************************************************************************
#
#DOCK TEST#5
./3tpi : complex Trypsinogen/ILE-VAL dipeptide
#
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 3tpi.IV.Prot.pdb -cL 3tpi.IV.notNative.pdb -i MdynPar_d21.inp -sa SAprotocol_long.inp -mn 3tpi -o 3tpi.out
#
Docking result potential energy file:
3tpi.LigDockFin.ePL.res:
#
NN   LigDockFinXXX.XXX.pdb      ePLtot  eVDW    eCoul   eHb     eSolv   eGeo    tempTAv
   1 3tpi.LigDockFin001.001.    -80.1   -36.5   -24.1   -22.3   -10.1    12.8    51.7 
   2 3tpi.LigDockFin001.002.    -79.8   -35.0   -23.8   -21.4   -10.6    11.0    51.7
   3 3tpi.LigDockFin001.003.    -77.7   -34.5   -24.2   -22.5   -10.3    13.9    51.7
   4 3tpi.LigDockFin002.001.    -47.9   -20.2   -13.8   -17.7    -4.8     8.5    51.9
   5 3tpi.LigDockFin002.002.    -45.9   -20.4   -17.1   -16.9    -4.0    12.5    51.9
   6 3tpi.LigDockFin002.003.    -44.1   -15.2   -19.0   -17.4    -3.4    11.0    51.9
   7 3tpi.LigDockFin003.001.    -54.0   -16.8   -21.2   -21.0    -6.5    11.5    49.1
   8 3tpi.LigDockFin003.002.    -53.9   -17.3   -21.0   -20.9    -6.4    11.7    49.1
   9 3tpi.LigDockFin003.003.    -52.8   -17.7   -20.5   -18.7    -5.6     9.7    49.1
  10 3tpi.LigDockFin004.001.    -81.8   -35.4   -24.5   -22.1   -10.5    10.7    50.4 best eP_mode/rmsd_mode
  11 3tpi.LigDockFin004.002.    -80.9   -36.4   -24.2   -22.4   -10.5    12.7    50.4 best eP_mode/rmsd_mode
  12 3tpi.LigDockFin004.003.    -72.0   -39.0   -17.8   -16.9   -10.8    12.5    50.4
  13 3tpi.LigDockFin005.001.    -40.9   -16.3   -16.4   -19.9   -10.9    22.7    49.4
  14 3tpi.LigDockFin005.002.    -39.6   -13.3   -16.1   -17.3    -7.8    14.9    49.4
  15 3tpi.LigDockFin005.003.    -38.3   -15.3   -12.8   -19.4    -1.8    11.0    49.4
  16 3tpi.LigDockFin006.001.    -43.1   -19.4   -11.1   -15.8    -9.1    12.3    52.0
  17 3tpi.LigDockFin006.002.    -41.4   -14.3    -9.6   -19.1   -12.4    13.9    52.0
  18 3tpi.LigDockFin006.003.    -37.9   -13.1   -14.6    -8.6    -9.4     7.9    52.0
  19 3tpi.LigDockFin007.001.    -41.1   -14.6   -22.9   -18.5    -3.3    18.2    49.0
  20 3tpi.LigDockFin007.002.    -40.7   -11.4   -23.3   -17.9    -3.4    15.3    49.0
  21 3tpi.LigDockFin007.003.    -40.0   -12.5   -23.7   -17.7    -2.5    16.5    49.0
...
#
****************************************************************************************
#DOCK TEST#6
./1hvr - complex HIV-1 protease/XK263 ligand : 1hvr PdB code
#
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 1hvr.P.pdb -cL 1hvr.Lig.pdb -i MdynPar_d21.inp -sa SAprotocol_long.inp -mn 1hvr -o 1hvr.out
#
Docking result potential energy file:
1hvr.ePL.LigDockFin.res:
NN   LigDockFinXXX.XXX.pdb      ePLtot  eVDW    eCoul   eHb     eSolv   eGeo    tempTAv
   1 1hvr.LigDockFin001.001.    -54.0   -74.9   -13.1   -13.8     9.3    38.5    49.3  best eP_mode/rmsd mode
   2 1hvr.LigDockFin001.002.    -53.8   -76.0   -14.2   -13.9     9.2    41.1    49.3  best eP_mode/rmsd mode
   3 1hvr.LigDockFin001.003.    -52.9   -76.6   -12.8   -14.3     9.3    41.5    49.3
   4 1hvr.LigDockFin002.001.    -16.9   -56.4    -9.8   -11.7    10.0    51.0    48.2
   5 1hvr.LigDockFin002.002.    -10.4   -37.7    -9.2   -13.7    12.2    37.9    48.2
   6 1hvr.LigDockFin002.003.    -10.1   -44.5    -9.8   -13.0    12.2    45.1    48.2
   7 1hvr.LigDockFin003.001.    -24.1   -56.5   -11.2    -9.9     9.2    44.3    49.8
   8 1hvr.LigDockFin003.002.    -17.9   -57.7    -7.3    -8.7     9.1    46.8    49.8
   9 1hvr.LigDockFin003.003.    -12.2   -40.8    -9.5   -17.4    12.4    43.1    49.8
  10 1hvr.LigDockFin004.001.     -3.6   -35.4    -8.1    -9.1    14.6    34.4    49.5
  11 1hvr.LigDockFin004.002.     -2.7   -33.5    -4.0   -16.5    15.7    35.6    49.5
  12 1hvr.LigDockFin004.003.     -2.4   -36.0    -9.8   -11.2    14.6    40.0    49.5
  13 1hvr.LigDockFin005.001.     -2.5   -29.9    -7.8    -9.9    15.4    29.7    50.4
  14 1hvr.LigDockFin005.002.     -0.8   -38.8    -3.2    -9.1    14.3    35.9    50.4
  15 1hvr.LigDockFin005.003.      0.4   -37.4    -4.4    -7.7    14.6    35.4    50.4
  16 1hvr.LigDockFin006.001.     -6.6   -42.2    -6.4   -10.0    14.0    38.0    49.1
  17 1hvr.LigDockFin006.002.     -5.8   -35.5    -6.9   -13.0    14.1    35.5    49.1
  18 1hvr.LigDockFin006.003.     -4.1   -38.7    -5.9    -9.8    14.4    35.9    49.1
  19 1hvr.LigDockFin007.001.     -3.5   -35.0    -6.1   -13.2    14.0    36.8    50.7
  20 1hvr.LigDockFin007.002.     -3.2   -35.4    -6.5   -13.2    14.5    37.4    50.7
  21 1hvr.LigDockFin007.003.      0.9   -30.9    -5.0   -11.0    14.5    33.3    50.7
...
#
*************************************************************************************
#
#DOCK TEST#7
 ./4phv
 Complex HIV-1 protease with inhibitor VAC : PDB code 4phv
 #
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 4phv.P.pdb -cL 4phv.Lig.pdb -i MdynPar_d23.inp -sa SAprotocol_long.inp -mn 4phv -o 4phv.out
#
Docking result potential energy file:
4phv.ePL.LigDockFin.res:
#
N   LigDockFinXXX.XXX.pdb      ePLtot  eVDW    eCoul   eHb     eSolv   eGeo    tempTAv
   1 4phv.LigDockFin001.001.    -57.1   -79.5   -12.2   -27.1     4.6    57.0    49.1 best eP_mode/rmsd_mode
   2 4phv.LigDockFin001.002.    -51.8   -81.4   -16.3   -24.6     4.6    65.9    49.1
   3 4phv.LigDockFin001.003.    -48.3   -68.8   -17.7   -32.5     6.6    64.1    49.1
   4 4phv.LigDockFin002.001.    -44.4   -74.5   -10.9   -20.7     6.2    55.4    49.9
   5 4phv.LigDockFin002.002.    -41.2   -62.0   -15.2   -32.4     6.7    61.8    49.9
   6 4phv.LigDockFin002.003.    -38.0   -60.6   -16.6   -27.3     6.8    59.7    49.9
   7 4phv.LigDockFin003.001.    -43.5   -69.4   -15.7   -28.6     6.9    63.2    48.9
   8 4phv.LigDockFin003.002.    -35.5   -67.0   -15.2   -25.2     7.5    64.4    48.9
   9 4phv.LigDockFin003.003.    -32.3   -59.6   -15.1   -23.6     7.5    58.5    48.9
  10 4phv.LigDockFin004.001.    -10.4   -31.4   -16.6   -28.5    14.8    51.3    49.9
  11 4phv.LigDockFin004.002.     -6.8   -32.0   -14.9   -28.2    14.0    54.4    49.9
  12 4phv.LigDockFin004.003.     -6.8   -41.0   -15.7   -19.4    11.0    58.3    49.9
  13 4phv.LigDockFin005.001.     -2.6   -44.5    -4.9   -19.2    11.8    54.1    50.1
  14 4phv.LigDockFin005.002.     -0.4   -39.1   -10.8   -18.1    13.0    54.5    50.1
  15 4phv.LigDockFin005.003.      1.0   -38.3    -9.9   -17.8    13.6    53.5    50.1
  16 4phv.LigDockFin006.001.    -20.0   -39.4   -20.1   -24.9    13.3    51.1    52.8
  17 4phv.LigDockFin006.002.    -18.5   -47.1   -12.5   -23.2    10.5    53.8    52.8
  18 4phv.LigDockFin006.003.    -16.0   -35.0   -19.1   -29.6    13.4    54.1    52.8
  19 4phv.LigDockFin007.001.    -28.8   -56.6   -13.0   -19.9     9.1    51.6    51.4
  20 4phv.LigDockFin007.002.    -27.6   -55.7   -15.1   -27.2     7.0    63.4    51.4
  21 4phv.LigDockFin007.003.    -24.2   -57.9   -10.1   -17.2     8.4    52.7    51.4

...
#
**********************************************************************************************
#DOCK TEST#8
 ./1hiv
  Complex HIV-1 protease with inhibitor NOA Ligand (119 atoms): PDB code 1hiv
#
Docking with option $doLigDock=21 provides  a small number (24) initial orientations for Lig and is unsufficient.
Docking with option $doLigDock=23 provides 72 initial Lig orientations and allows to find the same pose for two 
different initial orientations.
#
 Docking result potential energy file:
 1hiv.ePL.DockFin.res:
NN   LigDockFinXXX.XXX.pdb      ePLtot  eVDW    eCoul   eHb     eSolv   eGeo    tempTAv
   1 1hiv.LigDockFin001.001.    -84.9   -86.6   -28.0   -41.4    10.4    60.7    51.3 best eP_mode/rmsd
   2 1hiv.LigDockFin001.002.    -84.6   -91.0   -28.1   -41.3    10.4    65.5    51.3 best eP_mode/rmsd
   3 1hiv.LigDockFin001.003.    -70.4   -78.5   -29.8   -39.8     7.7    70.0    51.3
   4 1hiv.LigDockFin002.001.    -78.3   -80.3   -29.0   -40.8    10.9    61.0    50.1
   5 1hiv.LigDockFin002.002.    -74.1   -82.0   -28.9   -44.6    10.2    71.3    50.1
   6 1hiv.LigDockFin002.003.    -54.7   -67.2   -26.8   -40.8    12.0    68.1    50.1
   7 1hiv.LigDockFin003.001.    -15.0   -38.9   -22.9   -24.6    18.4    52.8    50.9
   8 1hiv.LigDockFin003.002.     -8.9   -37.8   -22.6   -22.9    19.4    55.0    50.9
   9 1hiv.LigDockFin003.003.     -8.3   -39.9   -19.9   -20.0    19.0    52.5    50.9
  10 1hiv.LigDockFin004.001.    -24.1   -48.2   -23.7   -32.6    16.3    64.1    49.9
  11 1hiv.LigDockFin004.002.    -23.9   -47.8   -20.0   -35.7    22.0    57.7    49.9
  12 1hiv.LigDockFin004.003.    -19.2   -45.8   -22.1   -30.0    17.2    61.5    49.9
  13 1hiv.LigDockFin005.001.    -18.8   -50.8   -21.0   -24.2    18.1    59.1    50.8
  14 1hiv.LigDockFin005.002.    -15.7   -42.8   -25.0   -29.7    18.7    63.2    50.8
  15 1hiv.LigDockFin005.003.    -14.1   -39.7   -23.7   -29.6    18.3    60.6    50.8
  16 1hiv.LigDockFin006.001.    -38.1   -61.4   -24.1   -28.0    17.4    58.0    50.9
  17 1hiv.LigDockFin006.002.    -34.9   -62.4   -25.7   -29.8    16.6    66.4    50.9
  18 1hiv.LigDockFin006.003.    -33.5   -60.3   -23.5   -31.2    15.1    66.3    50.9
  19 1hiv.LigDockFin007.001.    -40.2   -67.9   -24.6   -31.8     9.8    74.4    50.0
  20 1hiv.LigDockFin007.002.    -38.3   -75.4   -22.5   -20.7     6.6    73.6    50.0
  21 1hiv.LigDockFin007.003.    -36.2   -70.3   -20.6   -33.4     8.0    80.1    50.0
  22 1hiv.LigDockFin008.001.    -16.4   -45.3   -21.6   -22.2    14.7    57.9    51.6
 ....
  34 1hiv.LigDockFin012.001.    -84.4   -88.7   -29.7   -40.6    10.4    64.1    51.2 best eP_mode/rmsd
  35 1hiv.LigDockFin012.002.    -80.4   -84.1   -31.8   -42.1     8.5    69.0    51.2
  36 1hiv.LigDockFin012.003.    -69.9   -83.3   -31.2   -39.7     9.4    74.9    51.2

********************************************************************************************
RESUME :

1) all shown test example of docking module successevely find a set of docking modes, i.e. files
   LigDockFinXXX.XXX.pdb
2) the mode with minimal potential energy of Protein-Lig interactions in  the set of files 
   LigDockFinXXX.XXX.pdb are the mode close to the respective native ligand structure in the complex.
   The RMSD of the best docking mode from the native are withng 1 - 2 A.
3) The current docking method does not guarantee a finding of the best docking solution in the one RUN.
   The best docking solution can be obtained by docking with different set of initial Lig orientations
   by oprion $doLigDock=21(set24), 22(set144) or 23(set72 orientations)
*********************************************************************************************