Tue Oct 11 06:27:21 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 06:27:21 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 = 2101 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: 0.7306461 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): 25.72100 72.37800 ymin,ymax (A): -18.67300 30.05100 zmin,zma (A): 4.154000 46.44000 x,y,z range (A): 46.65700 48.72400 42.28600 scale (grids/A): 0.7306461 object centre (A): 49.04950 5.689000 25.29700 number of atom coordinates read : 2101 total number of charged atoms : 1974 net assigned charge : 6.500009 assigned positive charge : 320.1639 centred at (gu) : 89.22960 90.55843 90.20696 assigned negative charge : -313.6642 centred at (gu) : 89.36549 90.50436 90.28971 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7645 nv = 96 ne = 84 npr = 42238 no. pairs analyzed = 42238 no. exposed pairs = 2576 no. arc points = 17604 no. surface atoms = 877 nbur = 1224 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 599 mr = 4448 m= 5 mr = 141 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 0.2700000 number of dielectric boundary points 3660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1533 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5360025E-07 2.4600151E-08 midg,1,midg; midg,igrid,midg 4.3380819E-08 1.5143031E-07 1,midg,midg; igrid,midg,midg 2.3416506E-07 -1.7071430E-08 gauss-seidel spectral radius is 0.9902314 estimated iterations to convergence 82 setup time was (sec) 0.5200000 now iterating at: 06:27:22 rms-change max change #iterations 0.2250612 32.72600 at 10iterations 3.0263176E-02 3.669538 at 20iterations 4.2894040E-03 0.5887604 at 30iterations 7.5174193E-04 8.5727692E-02 at 40iterations 2.0391525E-04 2.2970200E-02 at 50iterations finished qdiffx linear iterations at : 06:27:25 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 2.0391525E-04 2.2970200E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 06:27:26 3.513u 0.192s 0:04.97 74.4% 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 06:27:26 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 = 2101 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: 2.191938 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): 25.72100 72.37800 ymin,ymax (A): -18.67300 30.05100 zmin,zma (A): 4.154000 46.44000 x,y,z range (A): 46.65700 48.72400 42.28600 scale (grids/A): 2.191938 object centre (A): 49.04950 5.689000 25.29700 number of atom coordinates read : 2101 total number of charged atoms : 1974 net assigned charge : 6.500009 assigned positive charge : 320.1639 centred at (gu) : 87.68884 91.67522 90.62106 assigned negative charge : -313.6642 centred at (gu) : 88.09660 91.51317 90.86929 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 81014 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17604 grid for indexing accessible points = 1.400000 m= 34690 mr = 58102 m= 7429 mr = 26703 m= 749 mr = 5153 m= 25 mr = 387 m= 0 mr = 4 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 33558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15706 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) : 0.7306461 object centre at (A) : 49.04950 5.689000 25.29700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8611772E-02 3.1265430E-02 midg,1,midg; midg,igrid,midg 5.3929124E-02 3.7189428E-02 1,midg,midg; igrid,midg,midg 4.9573842E-02 -6.6070959E-02 gauss-seidel spectral radius is 0.9988951 estimated iterations to convergence 238 setup time was (sec) 1.010000 now iterating at: 06:27:28 rms-change max change #iterations 4.895628 233.9768 at 10iterations 2.468323 79.17938 at 20iterations 1.250149 42.95690 at 30iterations 0.6329825 17.64457 at 40iterations 0.3200473 9.109773 at 50iterations 0.1624615 4.318347 at 60iterations 8.2474135E-02 2.341047 at 70iterations 4.1739520E-02 1.154093 at 80iterations 2.1293268E-02 0.5980911 at 90iterations 1.0901555E-02 0.3017426 at 100iterations 5.5952012E-03 0.1665382 at 110iterations 2.9515903E-03 9.4474792E-02 at 120iterations finished qdiffx linear iterations at : 06:27:35 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 2.9515903E-03 9.4474792E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.220000 DelPhi exited at 06:27:35 8.221u 0.218s 0:09.05 93.1% 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 06:27:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2101 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: 3.287907 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): 25.72100 72.37800 ymin,ymax (A): -18.67300 30.05100 zmin,zma (A): 4.154000 46.44000 x,y,z range (A): 46.65700 48.72400 42.28600 scale (grids/A): 3.287907 object centre (A): 49.04950 5.689000 25.29700 number of atom coordinates read : 2101 total number of charged atoms : 1974 net assigned charge : 6.500009 assigned positive charge : 320.1639 centred at (gu) : 86.53320 92.51292 90.93156 assigned negative charge : -313.6642 centred at (gu) : 87.14508 92.26955 91.30402 start vw surface at 0.1500000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 186127 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17604 grid for indexing accessible points = 1.400000 m= 105776 mr = 139002 m= 46275 mr = 88917 m= 14464 mr = 38646 m= 3132 mr = 11466 m= 398 mr = 2360 m= 19 mr = 242 m= 0 mr = 7 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.110000 number of dielectric boundary points 75551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 15792 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) : 2.191938 object centre at (A) : 49.04950 5.689000 25.29700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1393112 0.2560835 midg,1,midg; midg,igrid,midg 0.4237268 0.1627784 1,midg,midg; igrid,midg,midg 0.4829585 -0.7668593 gauss-seidel spectral radius is 0.9993132 estimated iterations to convergence 301 setup time was (sec) 2.460000 now iterating at: 06:27:38 rms-change max change #iterations 10.73494 403.6104 at 10iterations 6.400198 174.8760 at 20iterations 3.805038 84.65662 at 30iterations 2.265471 49.57325 at 40iterations 1.344936 26.74087 at 50iterations 0.7946426 16.95371 at 60iterations 0.4701678 9.098629 at 70iterations 0.2784035 5.043142 at 80iterations 0.1642079 3.133160 at 90iterations 9.7105779E-02 1.661469 at 100iterations 5.7475578E-02 0.9996948 at 110iterations 3.4187928E-02 0.6897087 at 120iterations 2.0471998E-02 0.3671646 at 130iterations 1.2455762E-02 0.2148720 at 140iterations 7.8081493E-03 0.1438217 at 150iterations 5.1040011E-03 9.2189789E-02 at 160iterations 3.5262399E-03 6.6799164E-02 at 170iterations 2.5979702E-03 5.0292969E-02 at 180iterations finished qdiffx linear iterations at : 06:27:49 total time elapsed so far: 13.69000 # loops : 180 mean,max change (kT/e) : 2.5979702E-03 5.0292969E-02 energy calculations done at 13.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.88000 DelPhi exited at 06:27:50 13.878u 0.215s 0:14.69 95.8% 0+0k 0+0io 0pf+0w