receptor = 1hsg_prot.pdbqt
ligand   = indinavir.pdbqt
num_modes = 50
out = dockingResult.pdbqt
log = docking.log
center_x = 16
center_y = 25
center_z = 4
size_x = 30
size_y = 30
size_z = 30
seed = 2009

 ############################################################
###All one needs to do is replacing:                        ##
###  * Protein structure file: E:\docking\1hsg_prot.pdb     ##
###  * Protein name: 1hsg                                   ##
###  * Docking result file: E:\docking\indinavir.pdbqt      ##
###  * Docking result name (normally ligand name): indinavir##
 ############################################################
# The following 4 lines: 
	# 1. load protein structure and rename it
	# 2. add hydrogen (`h_add` uses a primitive algorithm to add hydrogens onto a molecule.)
	# 3. hide protein display
	# 4. show cartoon display for protein
load E:\yunpan\docking\1hsg_prot.pdb, 1hsg
h_add 1hsg
hide everything, 1hsg
show cartoon, 1hsg
cmd.spectrum("count", selection="1hsg", byres=1)

# The following 6 lines: 
	# 1. load ligand structure and rename it
	# 2. add hydrogen
	# 3. hide ligand display
	# 4. show ligand in sticks mode
	# 5. Set width of stick to 0.15
	# 6. Set atom color: C-white;N-blue;O-red
load E:\yunpan\docking\indinavir.pdbqt, indinavir
h_add indinavir
hide everything, indinavir
show sticks, indinavir
set stick_radius, 0.15
util.cbaw indinavir

# The following 1 line:
	# 1. Select metal ions
select metals, symbol mg+ca+fe+zn

# The following 2 lines:
	# 1. Set hydrogen donator
	# 2. Set hydrogen accrptor 
	# `select` creates a named selection from an atom selection. 
	# `select name, (selection)`
select h_donator,  (elem n,o and (neighbor hydro))
select h_acceptor, (elem o or (elem n and not (neighbor hydro)))

# The following 4 lines:
	# 1. Create link between ligand_h_acceptor and prot_h_donator  within given distance 3.2
	# 2. Create link between ligand_h_donator  and prot_h_acceptor within given distance 3.2
	#    Set filter 3.6 for ideal geometry and filter 3.2 for minimally acceptable geometry
	# 3. Set red color for ligand_h_acceptor and prot_h_donator 
	# 4. Set blue color for ligand_h_donator  and prot_h_acceptor
	# `distance` creates a new distance object between two selections. It will display all distances within the cutoff. Distance is also used to make hydrogen bonds like `distance hbonds, all, all, 3.2, mode=2`.
	# distance [ name [, selection1 [, selection2 [, cutoff [, mode ]]]]]
distance LaccPdon, (indinavir and h_acceptor), (1hsg and h_donator), 3.2
distance LdonPacc, (indinavir and h_donator), (1hsg and h_acceptor), 3.2
color red, LaccPdon
color blue, LdonPacc
#distance Fe_C20, (fep and name C20), (heme and name fe))

# The following 6 lines:
	# 1. Select non-hydro atoms of ligands
	# 2. Select protein atoms within 5A of selected atoms in last step
	# 3. Label alpha-c(ca) of selected residues with residue name and residue position
	# 4. Set label color back
	# 5. Set background white
	# 6. Hidden hydrogenes
select sele, indinavir & not hydro
select sele, byres (sele expand 5) & 1hsg
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',    \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',    \
'GLY':'G', 'PRO':'P', 'CYS':'C'}
label name ca & sele, "%s-%s" % (one_letter[resn],resi)
bg white
set label_color, black
hide (hydro)

# The follwing 5 lines
	# 1. Comment out this line
	# 2. Create an object `surrounding_res` to represent selected protein atoms
	#    `create`: creates a new molecule object from a selection. It can also be used to create states in an   existing object. 
	#    `create name, (selection)`
	# 3. Display created surface
	# 4. Set color for surrounding_res
	# 5. Set transparency for surrounding_res
	#    Transparency is used to adjust the transparency of Surfaces and Slices.    
	#    `set transparency, F, selection`
#show surface, 1hsg
create surrounding_res, sele
show surface, surrounding_res
color grey80, surrounding_res
set transparency, 0.5, surrounding_res

# Copyright (c) 2010 Robert L. Campbell
from pymol import cmd

def list_hb(selection,selection2=None,cutoff=3.2,angle=55,mode=1,hb_list_name='hbonds'):
    """
    USAGE
  
    list_hb selection, [selection2 (default=None)], [cutoff (default=3.2)],
                       [angle (default=55)], [mode (default=1)],
                       [hb_list_name (default='hbonds')]
  
    The script automatically adds a requirement that atoms in the
    selection (and selection2 if used) must be either of the elements N or
    O.
  
    If mode is set to 0 instead of the default value 1, then no angle
    cutoff is used, otherwise the angle cutoff is used and defaults to 55
    degrees.
  
    e.g.
    To get a list of all H-bonds within chain A of an object
      list_hb 1abc & c. a &! r. hoh, cutoff=3.2, hb_list_name=abc-hbonds
  
    To get a list of H-bonds between chain B and everything else:
      list_hb 1tl9 & c. b, 1tl9 &! c. b
  
    """
    cutoff=float(cutoff)
    angle=float(angle)
    mode=float(mode)
    # ensure only N and O atoms are in the selection
    selection = selection + " & e. n+o"
    if not selection2:
        hb = cmd.find_pairs(selection,selection,mode=mode,cutoff=cutoff,angle=angle)
    else:
        selection2 = selection2 + " & e. n+o"
        hb = cmd.find_pairs(selection,selection2,mode=mode,cutoff=cutoff,angle=angle)
  
    # sort the list for easier reading
    hb.sort(lambda x,y:(cmp(x[0][1],y[0][1])))
  
    for pairs in hb:
        cmd.iterate("%s and index %s" % (pairs[0][0],pairs[0][1]), 'print "%1s/%3s`%s/%-4s " % (chain,resn,resi,name),')
        cmd.iterate("%s and index %s" % (pairs[1][0],pairs[1][1]), 'print "%1s/%3s`%s/%-4s " % (chain,resn,resi,name),')
        print "%.2f" % cmd.distance(hb_list_name,"%s and index %s" % (pairs[0][0],pairs[0][1]),"%s and index %s" % (pairs[1][0],pairs[1][1]))

#cmd.extend("list_hb",list_hb)
#if __name__ == "__main__":
cmd.load("E:/yunpan/docking/1hsg_prot.pdb", "1hsg")
cmd.h_add("(1hsg)")
cmd.load("E:/yunpan/docking/indinavir.pdbqt","indinavir")
cmd.h_add("(indinavir)")

h_donator  = "elem n,o & (neighbor hydro)"
h_acceptor = "elem o | (elem n & !(neighbor hydro))"

lacc = "indinavir & (elem o | (elem n & !(neighbor hydro)))"
ldon = "indinavir & (elem n,o & (neighbor hydro))"
pacc = "1hsg & (elem o | (elem n & !(neighbor hydro)))"
pdon = "1hsg & (elem n,o & (neighbor hydro))"

list_hb(ldon, pacc, hb_list_name="l2p_hbonds")
list_hb(lacc, pdon, hb_list_name="p2l_hbonds")

PyMOL>run E:/docking/list_hbonds.py
B/MK1`902/N4    B/GLY`27/O     3.03
B/MK1`902/O4    B/GLY`27/O     3.16
B/MK1`902/O2    A/ASP`25/OD1   2.77
B/MK1`902/O2    B/ASP`25/OD1   2.63

# color_h
# -------
 
# PyMOL command to color protein molecules according to the Eisenberg hydrophobicity scale
 
#
# Source: http://us.expasy.org/tools/pscale/Hphob.Eisenberg.html
# Amino acid scale: Normalized consensus hydrophobicity scale
# Author(s): Eisenberg D., Schwarz E., Komarony M., Wall R.
# Reference: J. Mol. Biol. 179:125-142 (1984)
#
# Amino acid scale values:
#
# Ala:  0.620
# Arg: -2.530
# Asn: -0.780
# Asp: -0.900
# Cys:  0.290
# Gln: -0.850
# Glu: -0.740
# Gly:  0.480
# His: -0.400
# Ile:  1.380
# Leu:  1.060
# Lys: -1.500
# Met:  0.640
# Phe:  1.190
# Pro:  0.120
# Ser: -0.180
# Thr: -0.050
# Trp:  0.810
# Tyr:  0.260
# Val:  1.080
#
# Usage:
# color_h (selection)
#
from pymol import cmd
 
def color_h(selection='all'):
        s = str(selection)
	print s
        cmd.set_color('color_ile',[0.996,0.062,0.062])
        cmd.set_color('color_phe',[0.996,0.109,0.109])
        cmd.set_color('color_val',[0.992,0.156,0.156])
        cmd.set_color('color_leu',[0.992,0.207,0.207])
        cmd.set_color('color_trp',[0.992,0.254,0.254])
        cmd.set_color('color_met',[0.988,0.301,0.301])
        cmd.set_color('color_ala',[0.988,0.348,0.348])
        cmd.set_color('color_gly',[0.984,0.394,0.394])
        cmd.set_color('color_cys',[0.984,0.445,0.445])
        cmd.set_color('color_tyr',[0.984,0.492,0.492])
        cmd.set_color('color_pro',[0.980,0.539,0.539])
        cmd.set_color('color_thr',[0.980,0.586,0.586])
        cmd.set_color('color_ser',[0.980,0.637,0.637])
        cmd.set_color('color_his',[0.977,0.684,0.684])
        cmd.set_color('color_glu',[0.977,0.730,0.730])
        cmd.set_color('color_asn',[0.973,0.777,0.777])
        cmd.set_color('color_gln',[0.973,0.824,0.824])
        cmd.set_color('color_asp',[0.973,0.875,0.875])
        cmd.set_color('color_lys',[0.899,0.922,0.922])
        cmd.set_color('color_arg',[0.899,0.969,0.969])
        cmd.color("color_ile","("+s+" and resn ile)")
        cmd.color("color_phe","("+s+" and resn phe)")
        cmd.color("color_val","("+s+" and resn val)")
        cmd.color("color_leu","("+s+" and resn leu)")
        cmd.color("color_trp","("+s+" and resn trp)")
        cmd.color("color_met","("+s+" and resn met)")
        cmd.color("color_ala","("+s+" and resn ala)")
        cmd.color("color_gly","("+s+" and resn gly)")
        cmd.color("color_cys","("+s+" and resn cys)")
        cmd.color("color_tyr","("+s+" and resn tyr)")
        cmd.color("color_pro","("+s+" and resn pro)")
        cmd.color("color_thr","("+s+" and resn thr)")
        cmd.color("color_ser","("+s+" and resn ser)")
        cmd.color("color_his","("+s+" and resn his)")
        cmd.color("color_glu","("+s+" and resn glu)")
        cmd.color("color_asn","("+s+" and resn asn)")
        cmd.color("color_gln","("+s+" and resn gln)")
        cmd.color("color_asp","("+s+" and resn asp)")
        cmd.color("color_lys","("+s+" and resn lys)")
        cmd.color("color_arg","("+s+" and resn arg)")
cmd.extend('color_h',color_h)
 
def color_h2(selection='all'):
        s = str(selection)
	print s
	cmd.set_color("color_ile2",[0.938,1,0.938])
	cmd.set_color("color_phe2",[0.891,1,0.891])
	cmd.set_color("color_val2",[0.844,1,0.844])
	cmd.set_color("color_leu2",[0.793,1,0.793])
	cmd.set_color("color_trp2",[0.746,1,0.746])
	cmd.set_color("color_met2",[0.699,1,0.699])
	cmd.set_color("color_ala2",[0.652,1,0.652])
	cmd.set_color("color_gly2",[0.606,1,0.606])
	cmd.set_color("color_cys2",[0.555,1,0.555])
	cmd.set_color("color_tyr2",[0.508,1,0.508])
	cmd.set_color("color_pro2",[0.461,1,0.461])
	cmd.set_color("color_thr2",[0.414,1,0.414])
	cmd.set_color("color_ser2",[0.363,1,0.363])
	cmd.set_color("color_his2",[0.316,1,0.316])
	cmd.set_color("color_glu2",[0.27,1,0.27])
	cmd.set_color("color_asn2",[0.223,1,0.223])
	cmd.set_color("color_gln2",[0.176,1,0.176])
	cmd.set_color("color_asp2",[0.125,1,0.125])
	cmd.set_color("color_lys2",[0.078,1,0.078])
	cmd.set_color("color_arg2",[0.031,1,0.031])
        cmd.color("color_ile2","("+s+" and resn ile)")
        cmd.color("color_phe2","("+s+" and resn phe)")
        cmd.color("color_val2","("+s+" and resn val)")
        cmd.color("color_leu2","("+s+" and resn leu)")
        cmd.color("color_trp2","("+s+" and resn trp)")
        cmd.color("color_met2","("+s+" and resn met)")
        cmd.color("color_ala2","("+s+" and resn ala)")
        cmd.color("color_gly2","("+s+" and resn gly)")
        cmd.color("color_cys2","("+s+" and resn cys)")
        cmd.color("color_tyr2","("+s+" and resn tyr)")
        cmd.color("color_pro2","("+s+" and resn pro)")
        cmd.color("color_thr2","("+s+" and resn thr)")
        cmd.color("color_ser2","("+s+" and resn ser)")
        cmd.color("color_his2","("+s+" and resn his)")
        cmd.color("color_glu2","("+s+" and resn glu)")
        cmd.color("color_asn2","("+s+" and resn asn)")
        cmd.color("color_gln2","("+s+" and resn gln)")
        cmd.color("color_asp2","("+s+" and resn asp)")
        cmd.color("color_lys2","("+s+" and resn lys)")
        cmd.color("color_arg2","("+s+" and resn arg)")
cmd.extend('color_h2',color_h2)

HEADER    HYDROLASE (ACID PROTEINASE)             31-MAR-95   1HSG              
TITLE     CRYSTAL STRUCTURE AT 1.9 ANGSTROMS RESOLUTION OF HUMAN                
TITLE    2 IMMUNODEFICIENCY VIRUS (HIV) II PROTEASE COMPLEXED WITH L-           
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: HIV-1 PROTEASE;                                            
COMPND   3 CHAIN: A, B;                                                         
COMPND   5 ENGINEERED: YES;                                                     
COMPND   6 OTHER_DETAILS: NY5 ISOLATE                                           
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1;                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    HYDROLASE (ACID PROTEINASE)                                           
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    Z.CHEN                                                                
REVDAT   3   24-FEB-09 1HSG    1       VERSN                                    
REVDAT   1   03-APR-96 1HSG    0                                                
JRNL        AUTH   Z.CHEN,Y.LI,E.CHEN,D.L.HALL,P.L.DARKE,C.CULBERSON,           
JRNL        TITL   CRYSTAL STRUCTURE AT 1.9-A RESOLUTION OF HUMAN               
JRNL        TITL 2 IMMUNODEFICIENCY VIRUS (HIV) II PROTEASE COMPLEXED           
JRNL        REF    J.BIOL.CHEM.                  V. 269 26344 1994              
JRNL        PMID   7929352                                                      
REMARK   1                                                                      
REMARK   3   PROGRAM     : X-PLOR                                               
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00                           
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MK1 B 902                 

DBREF  1HSG A    1    99  UNP    P03367   POL_HV1BR       69    167             
DBREF  1HSG B    1    99  UNP    P03367   POL_HV1BR       69    167             
SEQRES   1 A   99  PRO GLN ILE THR LEU TRP GLN ARG PRO LEU VAL THR ILE          
SEQRES   7 A   99  PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR          
SEQRES   8 A   99  GLN ILE GLY CYS THR LEU ASN PHE                              
SEQRES   1 B   99  PRO GLN ILE THR LEU TRP GLN ARG PRO LEU VAL THR ILE          
SEQRES   2 B   99  LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR          
SEQRES   8 B   99  GLN ILE GLY CYS THR LEU ASN PHE                              
HET    MK1  B 902      45                                                       
HETNAM     MK1 N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY                  
HETNAM   2 MK1  BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-              
HETNAM   3 MK1  4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE                       
HETSYN     MK1 INDINAVIR                                                        
FORMUL   3  MK1    C36 H47 N5 O4                                                
FORMUL   4  HOH   *127(H2 O)                                                    
HELIX    1   1 ARG A   87  LEU A   90  1                                   4    
HELIX    2   2 ARG B   87  LEU B   90  1                                   4    
SHEET    1   A 2 LEU A  10  ILE A  15  0                                        
SHEET    2   A 2 GLN A  18  LEU A  23 -1  N  ALA A  22   O  VAL A  11           
SHEET    1   B 4 VAL A  32  GLU A  34  0                                        
SITE     1 AC1 20 ARG A   8  ASP A  25  GLY A  27  GLY A  48                    
SITE     2 AC1 20 GLY A  49  VAL A  82  ARG B   8  ASP B  25                    
SITE     3 AC1 20 GLY B  27  ALA B  28  ASP B  29  ASP B  30                    
SITE     4 AC1 20 VAL B  32  GLY B  48  GLY B  49  ILE B  50                    
SITE     5 AC1 20 PRO B  81  HOH B 308  HOH B 313  HOH B 444                    
CRYST1   59.570   87.070   46.710  90.00  90.00  90.00 P 21 21 2     8          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      0.016787  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.011485  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.021409        0.00000                         

ATOM      1  N   PRO A   1      29.361  39.686   5.862  1.00 38.10           N  
ATOM      2  CA  PRO A   1      30.307  38.663   5.319  1.00 40.62           C  
ATOM      3  C   PRO A   1      29.760  38.071   4.022  1.00 42.64           C  
ATOM      4  O   PRO A   1      28.600  38.302   3.676  1.00 43.40           O  
ATOM      5  CB  PRO A   1      30.508  37.541   6.342  1.00 37.87           C  
ATOM    757  CZ  PHE A  99      20.700  32.221  -9.700  1.00 27.25           C  
TER     758      PHE A  99                                                      
ATOM    759  N   PRO B   1      22.659  36.727 -10.823  1.00 48.12           N  
ATOM    760  CA  PRO B   1      21.708  37.741 -10.269  1.00 43.36           C  
ATOM   1513  CE1 PHE B  99      25.450  37.240   6.756  1.00 37.02           C  
ATOM   1514  CE2 PHE B  99      25.473  38.988   8.409  1.00 37.11           C  
ATOM   1515  CZ  PHE B  99      25.658  37.663   8.073  1.00 36.24           C  
TER    1516      PHE B  99                                                      

HETATM 1517  N1  MK1 B 902       9.280  23.763   3.004  1.00 28.25           N  
HETATM 1518  C1  MK1 B 902       9.498  23.983   4.459  1.00 30.30           C  
HETATM 1519  C2  MK1 B 902      10.591  24.905   4.962  1.00 27.27           C  
HETATM 1560  C35 MK1 B 902       4.654  23.774   4.136  1.00 49.34           C  
HETATM 1561  C36 MK1 B 902       5.905  23.211   3.897  1.00 44.71           C  
HETATM 1562  O   HOH A 305      20.857  43.192  21.450  1.00 63.07           O  
HETATM 1563  O   HOH A 307      14.076  19.789  19.440  1.00 63.34           O  
HETATM 1687  O   HOH B 613      24.127 -10.994  -0.982  1.00 64.49           O  
HETATM 1688  O   HOH B 617      30.112  17.912  -4.791  1.00 54.09           O  

CONECT 1517 1518 1529 1555                                                      
CONECT 1518 1517 1519                                                           
CONECT 1519 1518 1520 1527                                                      
CONECT 1520 1519 1521 1522                                                      
CONECT 1561 1556 1560                                                           
MASTER      274    0    1    2   17    0    5    6 1686    2   45   16          
END                                                                             

REMARK   4 XXXX COMPLIES WITH FORMAT V. 2.0
ATOM      1  N   PRO A   1      29.361  39.686   5.862  1.00 38.10    -0.038 N 
ATOM      2  HN1 PRO A   1      28.682  40.038   5.187  1.00  0.00     0.280 HD
ATOM      3  HN2 PRO A   1      29.784  40.592   6.064  1.00  0.00     0.280 HD
ATOM      4  CA  PRO A   1      30.307  38.663   5.319  1.00 40.62     0.259 C 
ATOM      5  C   PRO A   1      29.760  38.071   4.022  1.00 42.64     0.259 C 
ATOM      6  O   PRO A   1      28.600  38.302   3.676  1.00 43.40    -0.271 OA
TER     923      PHE A  99 
ATOM    923  N   PRO B   1      22.659  36.727 -10.823  1.00 48.12    -0.038 N 
ATOM    924  HN1 PRO B   1      23.408  37.118 -11.394  1.00  0.00     0.280 HD
ATOM    925  HN2 PRO B   1      23.268  36.295 -10.128  1.00  0.00     0.280 HD
ATOM    926  CA  PRO B   1      21.708  37.741 -10.269  1.00 43.36     0.259 C 
ATOM   1844  CZ  PHE B  99      25.658  37.663   8.073  1.00 36.24     0.000 A 
TER    1845      PHE B  99 

REMARK  14 active torsions:
REMARK  status: ('A' for Active; 'I' for Inactive)
REMARK    1  A    between atoms: N1_1517  and  C31_1559 
REMARK    2  A    between atoms: C2_1519  and  C3_1520 
REMARK       I    between atoms: C3_1520  and  N2_1522 
REMARK    4  A    between atoms: N3_1528  and  C10_1531 
REMARK   13  A    between atoms: C23_1549  and  O4_1550 
REMARK   14  A    between atoms: C31_1559  and  C32_1560 
ROOT
HETATM    1  N1  MK1 B 902       9.280  23.763   3.004  1.00 28.25     0.146 N 
HETATM    2  C1  MK1 B 902       9.498  23.983   4.459  1.00 30.30     0.282 C 
HETATM    6  C9  MK1 B 902      10.440  23.182   2.493  1.00 27.47     0.274 C 
ENDROOT
BRANCH   1   7
HETATM    7  C31 MK1 B 902       8.033  23.100   2.604  1.00 36.25     0.278 C 
BRANCH   7   8
HETATM    8  C32 MK1 B 902       6.666  23.739   2.876  1.00 42.75     0.028 A 
HETATM    9  C36 MK1 B 902       5.905  23.211   3.897  1.00 44.71     0.001 A 
HETATM   10  C35 MK1 B 902       4.654  23.774   4.136  1.00 49.34     0.018 A 
HETATM   11  C34 MK1 B 902       4.207  24.839   3.348  1.00 50.60     0.072 A 
HETATM   12  N5  MK1 B 902       4.911  25.430   2.300  1.00 51.38    -0.351 N 
HETATM   13  C33 MK1 B 902       6.158  24.808   2.124  1.00 47.41     0.070 A 
HETATM   14  H5  MK1 B 902       4.567  26.208   1.737  1.00  0.00     0.166 HD
ENDBRANCH   7   8
ENDBRANCH   1   7
TORSDOF 14

#First make sure "~/bin" is in "PATH"

#AutoDock Vina
wget http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz
tar xvzf autodock_vina_1_1_2_linux_x86.tgz
ln -s `pwd`/autodock_vina_1_1_2_linux_x86/bin ~/bin

#AutoDockTools
wget http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL1.5.6/mgltools_x86_64Linux2_1.5.6.tar.gz
tar xvzf mgltools_x86_64Linux2_1.5.6.tar.gz
(cd mgltools_x86_64Linux2_1.5.6/; ./install.sh)
ln -s `pwd`/mgltools_x86_64Linux2_1.5.6/bin/pmv ~/bin/pmv
ln -s `pwd`/mgltools_x86_64Linux2_1.5.6/bin/adt ~/bin/adt
ln -s `pwd`/mgltools_x86_64Linux2_1.5.6/bin/vision ~/bin/vision
ln -s `pwd`/mgltools_x86_64Linux2_1.5.6/bin/pythonsh ~/bin/pythonsh

ln -s `pwd`/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py ~/bin
sed -i '1 s/python/pythonsh/' ~/bin/prepare_ligand4.py

ln -s `pwd`/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py ~/bin
sed -i '1 s/python/pythonsh/' ~/bin/prepare_receptor4.py

#PyMOL
尚未尝试编译

#Babel
yum install openbabel-2.2.3-1.el6.x86_64