Wed Dec 28 11:04:05 PST 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 Wed Dec 28 2011 at 11:04:05 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6438428 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): -6.110000 35.18200 ymin,ymax (A): -4.072000 49.69100 zmin,zma (A): -24.37300 30.92000 x,y,z range (A): 41.29200 53.76300 55.29300 scale (grids/A): 0.6438428 object centre (A): 14.53600 22.80950 3.273500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 291.4260 centred at (gu) : 90.77728 92.45683 90.22616 assigned negative charge : -287.4263 centred at (gu) : 90.87092 92.56693 90.17005 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5679 nv = 96 ne = 84 npr = 39959 no. pairs analyzed = 39959 no. exposed pairs = 2413 no. arc points = 17037 no. surface atoms = 827 nbur = 1135 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 285 mr = 3237 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2600000 number of dielectric boundary points 2695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1721 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6600 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3979028E-09 1.2712218E-08 midg,1,midg; midg,igrid,midg 1.0259270E-08 -6.8252168E-09 1,midg,midg; igrid,midg,midg 1.3265422E-08 -2.6506415E-09 gauss-seidel spectral radius is 0.9874446 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 11:04:06 rms-change max change #iterations 0.1289266 20.48066 at 10iterations 1.3071037E-02 1.840807 at 20iterations 1.3330344E-03 0.2779827 at 30iterations 1.3157527E-04 2.0690918E-02 at 40iterations 1.3199027E-05 1.9378662E-03 at 50iterations finished qdiffx linear iterations at : 11:04:13 total time elapsed so far: 6.780000 # loops : 50 mean,max change (kT/e) : 1.3199027E-05 1.9378662E-03 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 11:04:13 6.958u 0.685s 0:08.01 95.2% 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 Wed Dec 28 2011 at 11:04:13 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.931528 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): -6.110000 35.18200 ymin,ymax (A): -4.072000 49.69100 zmin,zma (A): -24.37300 30.92000 x,y,z range (A): 41.29200 53.76300 55.29300 scale (grids/A): 1.931528 object centre (A): 14.53600 22.80950 3.273500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 291.4260 centred at (gu) : 92.33179 97.37061 90.67830 assigned negative charge : -287.4263 centred at (gu) : 92.61299 97.70088 90.51041 start vw surface at 0.1000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 61007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17037 grid for indexing accessible points = 1.400000 m= 23070 mr = 42757 m= 3402 mr = 17816 m= 190 mr = 2181 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1672 time to turn everything in is 0.6100000 number of dielectric boundary points 24864 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 14422 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) : 0.6438428 object centre at (A) : 14.53600 22.80950 3.273500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4559453E-02 2.1622382E-02 midg,1,midg; midg,igrid,midg 2.7648231E-02 -2.8099439E-03 1,midg,midg; igrid,midg,midg 9.8573305E-03 -3.4485315E-03 gauss-seidel spectral radius is 0.9985939 estimated iterations to convergence 211 setup time was (sec) 1.040000 now iterating at: 11:04:15 rms-change max change #iterations 3.707941 193.5255 at 10iterations 1.725123 64.03386 at 20iterations 0.7982222 30.76049 at 30iterations 0.3703063 13.84879 at 40iterations 0.1712462 6.326141 at 50iterations 7.9137571E-02 2.758405 at 60iterations 3.6632903E-02 1.371243 at 70iterations 1.6904779E-02 0.5895600 at 80iterations 7.8495434E-03 0.2702475 at 90iterations 3.6286444E-03 0.1215286 at 100iterations 1.6824179E-03 5.7235718E-02 at 110iterations 7.8112195E-04 2.5502682E-02 at 120iterations finished qdiffx linear iterations at : 11:04:32 total time elapsed so far: 17.61000 # loops : 120 mean,max change (kT/e) : 7.8112195E-04 2.5502682E-02 energy calculations done at 17.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.79000 DelPhi exited at 11:04:32 17.795u 0.799s 0:18.99 97.8% 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 Wed Dec 28 2011 at 11:04:32 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.897293 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): -6.110000 35.18200 ymin,ymax (A): -4.072000 49.69100 zmin,zma (A): -24.37300 30.92000 x,y,z range (A): 41.29200 53.76300 55.29300 scale (grids/A): 2.897293 object centre (A): 14.53600 22.80950 3.273500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 291.4260 centred at (gu) : 93.49771 101.0559 91.01752 assigned negative charge : -287.4263 centred at (gu) : 93.91948 101.5515 90.76568 start vw surface at 0.1100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 140935 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17037 grid for indexing accessible points = 1.400000 m= 73937 mr = 103212 m= 27223 mr = 61960 m= 6037 mr = 22698 m= 750 mr = 4574 m= 32 mr = 477 m= 0 mr = 11 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 5957 time to turn everything in is 1.490000 number of dielectric boundary points 55982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 14640 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) : 1.931528 object centre at (A) : 14.53600 22.80950 3.273500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9918717 7.2463594E-02 midg,1,midg; midg,igrid,midg 0.2486732 -5.7927169E-02 1,midg,midg; igrid,midg,midg 6.4153463E-02 -2.4375292E-02 gauss-seidel spectral radius is 0.9992335 estimated iterations to convergence 285 setup time was (sec) 1.860000 now iterating at: 11:04:35 rms-change max change #iterations 8.745347 381.6083 at 10iterations 5.065154 146.4055 at 20iterations 2.904177 64.12048 at 30iterations 1.660477 40.84304 at 40iterations 0.9489646 23.36190 at 50iterations 0.5425463 12.57041 at 60iterations 0.3082370 6.435656 at 70iterations 0.1755001 3.657921 at 80iterations 0.1001526 2.282738 at 90iterations 5.6780592E-02 1.134063 at 100iterations 3.2348152E-02 0.6513519 at 110iterations 1.8356156E-02 0.3587036 at 120iterations 1.0419218E-02 0.2187653 at 130iterations 5.9265215E-03 0.1191626 at 140iterations 3.3700960E-03 6.6652298E-02 at 150iterations 1.9109375E-03 3.7833214E-02 at 160iterations 1.0867644E-03 2.0793915E-02 at 170iterations 6.1689119E-04 1.1634827E-02 at 180iterations finished qdiffx linear iterations at : 11:05:02 total time elapsed so far: 29.27000 # loops : 180 mean,max change (kT/e) : 6.1689119E-04 1.1634827E-02 energy calculations done at 29.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.44000 DelPhi exited at 11:05:03 29.447u 0.775s 0:30.47 99.1% 0+0k 0+0io 0pf+0w