Sun Oct 9 12:26:31 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 12:26:31 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2390 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6715587 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -6.435000 43.89100 ymin,ymax (A): -14.25800 38.75300 zmin,zma (A): 3.169000 45.37800 x,y,z range (A): 50.32600 53.01100 42.20900 scale (grids/A): 0.6715587 object centre (A): 18.72800 12.24750 24.27350 number of atom coordinates read : 2390 total number of charged atoms : 2248 net assigned charge : 3.500024 assigned positive charge : 367.4081 centred at (gu) : 89.43525 90.47719 90.18781 assigned negative charge : -363.9084 centred at (gu) : 89.46497 90.64707 90.28397 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7140 nv = 96 ne = 84 npr = 48518 no. pairs analyzed = 48518 no. exposed pairs = 2963 no. arc points = 20936 no. surface atoms = 990 nbur = 1400 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 3894 m= 3 mr = 60 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1957 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8294 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4646927E-08 -1.2224033E-08 midg,1,midg; midg,igrid,midg 4.8766122E-08 -3.3830069E-08 1,midg,midg; igrid,midg,midg 2.2123530E-08 4.5021387E-09 gauss-seidel spectral radius is 0.9884829 estimated iterations to convergence 76 setup time was (sec) 0.5700000 now iterating at: 12:26:32 rms-change max change #iterations 0.1763399 28.14292 at 10iterations 1.9918267E-02 2.531292 at 20iterations 2.5820828E-03 0.3276792 at 30iterations 5.4179737E-04 8.1209183E-02 at 40iterations 1.6207951E-04 2.4702072E-02 at 50iterations finished qdiffx linear iterations at : 12:26:34 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.6207951E-04 2.4702072E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 12:26:35 3.596u 0.179s 0:04.03 93.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 12:26:35 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2390 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.014676 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -6.435000 43.89100 ymin,ymax (A): -14.25800 38.75300 zmin,zma (A): 3.169000 45.37800 x,y,z range (A): 50.32600 53.01100 42.20900 scale (grids/A): 2.014676 object centre (A): 18.72800 12.24750 24.27350 number of atom coordinates read : 2390 total number of charged atoms : 2248 net assigned charge : 3.500024 assigned positive charge : 367.4081 centred at (gu) : 88.30524 91.43118 90.56269 assigned negative charge : -363.9084 centred at (gu) : 88.39484 91.94085 90.85166 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20936 grid for indexing accessible points = 1.400000 m= 28301 mr = 53010 m= 4796 mr = 20771 m= 337 mr = 2961 m= 3 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.5900000 number of dielectric boundary points 33026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17757 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6715587 object centre at (A) : 18.72800 12.24750 24.27350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6342332E-02 1.1029881E-02 midg,1,midg; midg,igrid,midg 1.8791690E-02 -4.8626792E-02 1,midg,midg; igrid,midg,midg 3.1253804E-02 -1.2231761E-02 gauss-seidel spectral radius is 0.9987542 estimated iterations to convergence 224 setup time was (sec) 0.8800000 now iterating at: 12:26:36 rms-change max change #iterations 4.570688 203.0590 at 10iterations 2.206242 69.83842 at 20iterations 1.069341 33.00712 at 30iterations 0.5187068 18.37105 at 40iterations 0.2506169 8.246979 at 50iterations 0.1215912 3.733269 at 60iterations 5.8978148E-02 1.932489 at 70iterations 2.8656073E-02 0.8535080 at 80iterations 1.4104834E-02 0.4736557 at 90iterations 6.9439178E-03 0.2197127 at 100iterations 3.4837769E-03 0.1098557 at 110iterations 1.8000361E-03 5.8238983E-02 at 120iterations finished qdiffx linear iterations at : 12:26:43 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 1.8000361E-03 5.8238983E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 12:26:44 8.152u 0.247s 0:08.67 96.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 12:26:44 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2390 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.022014 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -6.435000 43.89100 ymin,ymax (A): -14.25800 38.75300 zmin,zma (A): 3.169000 45.37800 x,y,z range (A): 50.32600 53.01100 42.20900 scale (grids/A): 3.022014 object centre (A): 18.72800 12.24750 24.27350 number of atom coordinates read : 2390 total number of charged atoms : 2248 net assigned charge : 3.500024 assigned positive charge : 367.4081 centred at (gu) : 87.45769 92.14652 90.84401 assigned negative charge : -363.9084 centred at (gu) : 87.59219 92.91128 91.27742 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 176505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20936 grid for indexing accessible points = 1.400000 m= 91339 mr = 128264 m= 33679 mr = 74647 m= 8635 mr = 26793 m= 1476 mr = 6363 m= 97 mr = 1012 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 105 time to turn everything in is 1.530000 number of dielectric boundary points 74610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 17979 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.014676 object centre at (A) : 18.72800 12.24750 24.27350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4295928 1.9329330E-02 midg,1,midg; midg,igrid,midg 0.4246562 -0.5678231 1,midg,midg; igrid,midg,midg 0.3147801 -0.2894817 gauss-seidel spectral radius is 0.9992784 estimated iterations to convergence 294 setup time was (sec) 1.870000 now iterating at: 12:26:46 rms-change max change #iterations 10.43870 407.6035 at 10iterations 6.108053 135.0613 at 20iterations 3.578339 76.68730 at 30iterations 2.094097 39.74680 at 40iterations 1.217006 22.88031 at 50iterations 0.7085649 12.98403 at 60iterations 0.4123665 7.712102 at 70iterations 0.2398284 4.727629 at 80iterations 0.1395790 2.784923 at 90iterations 8.1093989E-02 1.640537 at 100iterations 4.7197819E-02 0.7904854 at 110iterations 2.7538378E-02 0.5190659 at 120iterations 1.6212709E-02 0.3039627 at 130iterations 9.6386643E-03 0.1683578 at 140iterations 5.8626235E-03 0.1330738 at 150iterations 3.7020184E-03 7.3384285E-02 at 160iterations 2.4693541E-03 5.3398132E-02 at 170iterations 1.7470906E-03 3.8697243E-02 at 180iterations finished qdiffx linear iterations at : 12:26:59 total time elapsed so far: 14.90000 # loops : 180 mean,max change (kT/e) : 1.7470906E-03 3.8697243E-02 energy calculations done at 14.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.09000 DelPhi exited at 12:26:59 15.093u 0.236s 0:15.60 98.2% 0+0k 0+0io 0pf+0w