Sat Oct 8 19:12:28 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 Sat Oct 8 2011 at 19:12:28 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6242548 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): -32.00200 18.27800 ymin,ymax (A): -24.32800 23.29400 zmin,zma (A): -12.46000 44.56800 x,y,z range (A): 50.28000 47.62200 57.02800 scale (grids/A): 0.6242548 object centre (A): -6.862000 -0.5170002 16.05400 number of atom coordinates read : 2595 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.32018 89.24975 89.89909 assigned negative charge : -388.8955 centred at (gu) : 88.21268 89.29465 89.78927 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6911 nv = 96 ne = 84 npr = 52337 no. pairs analyzed = 52337 no. exposed pairs = 3103 no. arc points = 22440 no. surface atoms = 1049 nbur = 1546 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 3917 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2221 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8296 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1867354E-09 1.2118167E-08 midg,1,midg; midg,igrid,midg 8.9518242E-09 7.6425050E-10 1,midg,midg; igrid,midg,midg -5.8349845E-09 8.4879925E-09 gauss-seidel spectral radius is 0.9867117 estimated iterations to convergence 71 setup time was (sec) 0.6700000 now iterating at: 19:12:29 rms-change max change #iterations 0.1320028 19.75068 at 10iterations 1.2357568E-02 1.711473 at 20iterations 1.1539451E-03 0.1727600 at 30iterations 1.0816738E-04 1.6716003E-02 at 40iterations 1.0585485E-05 1.6517639E-03 at 50iterations finished qdiffx linear iterations at : 19:12:33 total time elapsed so far: 4.670000 # loops : 50 mean,max change (kT/e) : 1.0585485E-05 1.6517639E-03 energy calculations done at 4.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.900000 DelPhi exited at 19:12:34 4.906u 0.399s 0:05.58 94.8% 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 Sat Oct 8 2011 at 19:12:34 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.872764 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): -32.00200 18.27800 ymin,ymax (A): -24.32800 23.29400 zmin,zma (A): -12.46000 44.56800 x,y,z range (A): 50.28000 47.62200 57.02800 scale (grids/A): 1.872764 object centre (A): -6.862000 -0.5170002 16.05400 number of atom coordinates read : 2595 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 84.96004 87.74892 89.69698 assigned negative charge : -388.8955 centred at (gu) : 84.63792 87.88375 89.36768 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 74146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22440 grid for indexing accessible points = 1.400000 m= 28094 mr = 51969 m= 4651 mr = 21318 m= 256 mr = 3067 m= 2 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 894 time to turn everything in is 0.7600000 number of dielectric boundary points 30701 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 19324 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) : 0.6242548 object centre at (A) : -6.862000 -0.5170002 16.05400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4604957E-02 2.5835618E-02 midg,1,midg; midg,igrid,midg 1.5236515E-02 2.6364762E-03 1,midg,midg; igrid,midg,midg -4.9608280E-03 3.5350375E-02 gauss-seidel spectral radius is 0.9985938 estimated iterations to convergence 211 setup time was (sec) 1.070000 now iterating at: 19:12:35 rms-change max change #iterations 4.090399 186.4480 at 10iterations 1.897337 63.88673 at 20iterations 0.8754138 29.00251 at 30iterations 0.4046192 13.19290 at 40iterations 0.1878865 6.529884 at 50iterations 8.6949028E-02 3.134454 at 60iterations 4.0170781E-02 1.229424 at 70iterations 1.8599194E-02 0.6091270 at 80iterations 8.6330846E-03 0.2634335 at 90iterations 3.9888839E-03 0.1273613 at 100iterations 1.8561974E-03 5.8225632E-02 at 110iterations 8.6149917E-04 2.8553009E-02 at 120iterations finished qdiffx linear iterations at : 19:12:44 total time elapsed so far: 10.06000 # loops : 120 mean,max change (kT/e) : 8.6149917E-04 2.8553009E-02 energy calculations done at 10.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.28000 DelPhi exited at 19:12:45 10.283u 0.465s 0:11.07 97.0% 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 Sat Oct 8 2011 at 19:12:45 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.809146 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): -32.00200 18.27800 ymin,ymax (A): -24.32800 23.29400 zmin,zma (A): -12.46000 44.56800 x,y,z range (A): 50.28000 47.62200 57.02800 scale (grids/A): 2.809146 object centre (A): -6.862000 -0.5170002 16.05400 number of atom coordinates read : 2595 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 82.43979 86.62317 89.54536 assigned negative charge : -388.8955 centred at (gu) : 81.95685 86.82559 89.05149 start vw surface at 0.1600000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 170771 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22440 grid for indexing accessible points = 1.400000 m= 89890 mr = 124846 m= 33787 mr = 74789 m= 8572 mr = 27761 m= 1220 mr = 6717 m= 43 mr = 815 m= 0 mr = 15 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 3152 time to turn everything in is 1.970000 number of dielectric boundary points 69340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 19723 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) : 1.872764 object centre at (A) : -6.862000 -0.5170002 16.05400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8839318E-02 0.2753545 midg,1,midg; midg,igrid,midg 0.1923441 2.0351840E-02 1,midg,midg; igrid,midg,midg -5.0179224E-02 0.4310016 gauss-seidel spectral radius is 0.9992453 estimated iterations to convergence 287 setup time was (sec) 2.340000 now iterating at: 19:12:48 rms-change max change #iterations 9.606232 442.1238 at 10iterations 5.545698 125.1570 at 20iterations 3.183549 90.91484 at 30iterations 1.822391 35.07393 at 40iterations 1.044724 21.34962 at 50iterations 0.5969024 11.17454 at 60iterations 0.3410917 5.925932 at 70iterations 0.1950991 3.349995 at 80iterations 0.1109681 2.007986 at 90iterations 6.3454807E-02 1.147869 at 100iterations 3.6281150E-02 0.6754742 at 110iterations 2.0661885E-02 0.3638077 at 120iterations 1.1815717E-02 0.2059002 at 130iterations 6.7350469E-03 0.1266041 at 140iterations 3.8475171E-03 6.7958832E-02 at 150iterations 2.1977029E-03 3.9710999E-02 at 160iterations 1.2534583E-03 2.2925377E-02 at 170iterations 7.1538484E-04 1.2292385E-02 at 180iterations finished qdiffx linear iterations at : 19:13:04 total time elapsed so far: 18.68000 # loops : 180 mean,max change (kT/e) : 7.1538484E-04 1.2292385E-02 energy calculations done at 18.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.89000 DelPhi exited at 19:13:05 18.891u 0.503s 0:19.66 98.6% 0+0k 0+0io 0pf+0w