Tue Oct 11 06:24:05 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+sph.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 = amb.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 Tue Oct 11 2011 at 06:24:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2036 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: 0.7352638 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): -44.62500 3.793000 ymin,ymax (A): 9.657001 57.33400 zmin,zma (A): 21.14000 63.70100 x,y,z range (A): 48.41800 47.67700 42.56100 scale (grids/A): 0.7352638 object centre (A): -20.41600 33.49550 42.42050 number of atom coordinates read : 2036 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 89.00116 88.79173 90.14129 assigned negative charge : -302.7272 centred at (gu) : 89.12383 88.90604 90.22105 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7600 nv = 96 ne = 84 npr = 40635 no. pairs analyzed = 40635 no. exposed pairs = 2476 no. arc points = 16872 no. surface atoms = 849 nbur = 1187 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 576 mr = 4466 m= 2 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1553 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 8177 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8080257E-07 4.7823665E-08 midg,1,midg; midg,igrid,midg 2.6993419E-07 1.4129523E-08 1,midg,midg; igrid,midg,midg 2.6809349E-07 8.3121749E-09 gauss-seidel spectral radius is 0.9903485 estimated iterations to convergence 83 setup time was (sec) 0.4700000 now iterating at: 06:24:05 rms-change max change #iterations 0.2321715 29.80094 at 10iterations 3.1120032E-02 4.029564 at 20iterations 4.3171234E-03 0.6015444 at 30iterations 6.8574597E-04 9.2842102E-02 at 40iterations 1.5794279E-04 2.0187378E-02 at 50iterations finished qdiffx linear iterations at : 06:24:08 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.5794279E-04 2.0187378E-02 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 06:24:09 3.173u 0.184s 0:03.85 87.0% 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 Tue Oct 11 2011 at 06:24:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2036 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: 2.205791 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): -44.62500 3.793000 ymin,ymax (A): 9.657001 57.33400 zmin,zma (A): 21.14000 63.70100 x,y,z range (A): 48.41800 47.67700 42.56100 scale (grids/A): 2.205791 object centre (A): -20.41600 33.49550 42.42050 number of atom coordinates read : 2036 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 87.00353 86.37543 90.42377 assigned negative charge : -302.7272 centred at (gu) : 87.37154 86.71836 90.66332 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 79811 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16872 grid for indexing accessible points = 1.400000 m= 34058 mr = 56949 m= 7203 mr = 26329 m= 713 mr = 5037 m= 23 mr = 384 m= 0 mr = 3 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 33106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15287 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) : 0.7352638 object centre at (A) : -20.41600 33.49550 42.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4131858E-02 2.8177122E-02 midg,1,midg; midg,igrid,midg 4.8419792E-02 -3.2571897E-02 1,midg,midg; igrid,midg,midg 0.1147557 4.4115048E-02 gauss-seidel spectral radius is 0.9989004 estimated iterations to convergence 239 setup time was (sec) 0.9000000 now iterating at: 06:24:10 rms-change max change #iterations 4.876367 223.9290 at 10iterations 2.465930 88.40767 at 20iterations 1.253353 37.89892 at 30iterations 0.6352025 20.03072 at 40iterations 0.3218953 9.144135 at 50iterations 0.1635412 4.431606 at 60iterations 8.3252102E-02 2.457111 at 70iterations 4.2225804E-02 1.249947 at 80iterations 2.1504812E-02 0.6180744 at 90iterations 1.0959508E-02 0.3070297 at 100iterations 5.6109284E-03 0.1563835 at 110iterations 2.9288537E-03 7.6244831E-02 at 120iterations finished qdiffx linear iterations at : 06:24:17 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.9288537E-03 7.6244831E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 06:24:17 7.892u 0.221s 0:08.67 93.5% 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 Tue Oct 11 2011 at 06:24:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2036 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: 3.308687 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): -44.62500 3.793000 ymin,ymax (A): 9.657001 57.33400 zmin,zma (A): 21.14000 63.70100 x,y,z range (A): 48.41800 47.67700 42.56100 scale (grids/A): 3.308687 object centre (A): -20.41600 33.49550 42.42050 number of atom coordinates read : 2036 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 85.50533 84.56322 90.63571 assigned negative charge : -302.7272 centred at (gu) : 86.05745 85.07756 90.99483 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 183251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16872 grid for indexing accessible points = 1.400000 m= 103454 mr = 136210 m= 45354 mr = 87211 m= 13824 mr = 37875 m= 2916 mr = 10919 m= 384 mr = 2143 m= 20 mr = 246 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.890000 number of dielectric boundary points 74593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 15366 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) : 2.205791 object centre at (A) : -20.41600 33.49550 42.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1685549 0.2295527 midg,1,midg; midg,igrid,midg 0.4344489 -0.4281820 1,midg,midg; igrid,midg,midg 0.8512548 0.3360429 gauss-seidel spectral radius is 0.9993149 estimated iterations to convergence 301 setup time was (sec) 2.200000 now iterating at: 06:24:20 rms-change max change #iterations 10.70853 381.8358 at 10iterations 6.388936 170.6164 at 20iterations 3.815794 72.34023 at 30iterations 2.271863 39.79723 at 40iterations 1.349801 23.31736 at 50iterations 0.7992736 13.55206 at 60iterations 0.4736605 8.115295 at 70iterations 0.2801497 5.132743 at 80iterations 0.1653601 2.811241 at 90iterations 9.8056071E-02 1.790537 at 100iterations 5.7903536E-02 0.9197099 at 110iterations 3.4390435E-02 0.6449251 at 120iterations 2.0487016E-02 0.3610268 at 130iterations 1.2367718E-02 0.2208424 at 140iterations 7.6162140E-03 0.1266060 at 150iterations 4.8375013E-03 9.8815918E-02 at 160iterations 3.2259643E-03 6.5629959E-02 at 170iterations 2.2921397E-03 3.9314270E-02 at 180iterations finished qdiffx linear iterations at : 06:24:31 total time elapsed so far: 13.26000 # loops : 180 mean,max change (kT/e) : 2.2921397E-03 3.9314270E-02 energy calculations done at 13.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.44000 DelPhi exited at 06:24:32 13.441u 0.239s 0:14.21 96.1% 0+0k 0+0io 0pf+0w