Mon Oct 10 19:55:28 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 Mon Oct 10 2011 at 19:55:28 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2592 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: 0.6076434 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): -12.29300 45.36900 ymin,ymax (A): -16.87700 38.37200 zmin,zma (A): -12.59400 45.99300 x,y,z range (A): 57.66200 55.24900 58.58700 scale (grids/A): 0.6076434 object centre (A): 16.53800 10.74750 16.69950 number of atom coordinates read : 2592 total number of charged atoms : 2455 net assigned charge : 1.000011 assigned positive charge : 383.3228 centred at (gu) : 89.75570 90.12034 90.15297 assigned negative charge : -382.3239 centred at (gu) : 89.72968 90.12589 90.10892 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6605 nv = 96 ne = 84 npr = 50854 no. pairs analyzed = 50854 no. exposed pairs = 3738 no. arc points = 26614 no. surface atoms = 1242 nbur = 1350 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3124 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2604 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7951 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4127876E-09 2.6299314E-09 midg,1,midg; midg,igrid,midg 7.7969953E-10 3.0317346E-10 1,midg,midg; igrid,midg,midg -6.7648881E-10 1.6353703E-09 gauss-seidel spectral radius is 0.9859958 estimated iterations to convergence 69 setup time was (sec) 0.5200000 now iterating at: 19:55:29 rms-change max change #iterations 0.1115463 17.01801 at 10iterations 9.6380524E-03 1.348331 at 20iterations 8.4400224E-04 0.1211395 at 30iterations 7.8508419E-05 1.1281013E-02 at 40iterations 8.4945250E-06 1.2512207E-03 at 50iterations finished qdiffx linear iterations at : 19:55:31 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 8.4945250E-06 1.2512207E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 19:55:32 3.443u 0.234s 0:04.18 87.7% 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 Mon Oct 10 2011 at 19:55:32 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2592 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: 1.822930 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): -12.29300 45.36900 ymin,ymax (A): -16.87700 38.37200 zmin,zma (A): -12.59400 45.99300 x,y,z range (A): 57.66200 55.24900 58.58700 scale (grids/A): 1.822930 object centre (A): 16.53800 10.74750 16.69950 number of atom coordinates read : 2592 total number of charged atoms : 2455 net assigned charge : 1.000011 assigned positive charge : 383.3228 centred at (gu) : 89.26667 90.36049 90.45826 assigned negative charge : -382.3239 centred at (gu) : 89.18909 90.37775 90.32684 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70368 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26614 grid for indexing accessible points = 1.400000 m= 24104 mr = 45055 m= 3674 mr = 16413 m= 187 mr = 1942 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 34882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19205 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) : 0.6076434 object centre at (A) : 16.53800 10.74750 16.69950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5670807E-03 -1.2516837E-02 midg,1,midg; midg,igrid,midg 1.7098678E-02 4.3108040E-03 1,midg,midg; igrid,midg,midg 1.3866285E-02 4.3289531E-03 gauss-seidel spectral radius is 0.9985397 estimated iterations to convergence 207 setup time was (sec) 0.8200000 now iterating at: 19:55:33 rms-change max change #iterations 3.870017 181.2264 at 10iterations 1.751042 67.64313 at 20iterations 0.7964053 27.74733 at 30iterations 0.3628681 12.32089 at 40iterations 0.1649889 5.963654 at 50iterations 7.4995346E-02 2.493885 at 60iterations 3.4176007E-02 1.291044 at 70iterations 1.5589871E-02 0.4953842 at 80iterations 7.1115047E-03 0.2327919 at 90iterations 3.2547659E-03 0.1131320 at 100iterations 1.4797746E-03 4.8339844E-02 at 110iterations 6.7740993E-04 2.3035049E-02 at 120iterations finished qdiffx linear iterations at : 19:55:40 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 6.7740993E-04 2.3035049E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 19:55:41 7.903u 0.240s 0:08.56 95.0% 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 Mon Oct 10 2011 at 19:55:41 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2592 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: 2.734395 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): -12.29300 45.36900 ymin,ymax (A): -16.87700 38.37200 zmin,zma (A): -12.59400 45.99300 x,y,z range (A): 57.66200 55.24900 58.58700 scale (grids/A): 2.734395 object centre (A): 16.53800 10.74750 16.69950 number of atom coordinates read : 2592 total number of charged atoms : 2455 net assigned charge : 1.000011 assigned positive charge : 383.3228 centred at (gu) : 88.89988 90.54052 90.68741 assigned negative charge : -382.3239 centred at (gu) : 88.78364 90.56660 90.49028 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 162503 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26614 grid for indexing accessible points = 1.400000 m= 77349 mr = 110243 m= 27594 mr = 60120 m= 6292 mr = 20868 m= 714 mr = 4181 m= 28 mr = 373 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 78695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 19636 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) : 1.822930 object centre at (A) : 16.53800 10.74750 16.69950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5874088E-02 -0.1180699 midg,1,midg; midg,igrid,midg 0.2723274 6.1254863E-02 1,midg,midg; igrid,midg,midg 0.2206590 2.9957324E-02 gauss-seidel spectral radius is 0.9992471 estimated iterations to convergence 288 setup time was (sec) 1.610000 now iterating at: 19:55:43 rms-change max change #iterations 9.572109 325.2983 at 10iterations 5.675713 186.3282 at 20iterations 3.323209 77.00164 at 30iterations 1.935423 44.28490 at 40iterations 1.124953 22.11530 at 50iterations 0.6488460 15.17044 at 60iterations 0.3743592 9.257141 at 70iterations 0.2151305 4.357258 at 80iterations 0.1235852 2.473552 at 90iterations 7.1035169E-02 1.327562 at 100iterations 4.0640000E-02 0.7940784 at 110iterations 2.3320094E-02 0.4436951 at 120iterations 1.3352207E-02 0.2572021 at 130iterations 7.6270103E-03 0.1389008 at 140iterations 4.3717436E-03 8.0021858E-02 at 150iterations 2.5042628E-03 5.1309586E-02 at 160iterations 1.4348265E-03 2.8726578E-02 at 170iterations 8.2563021E-04 1.7021179E-02 at 180iterations finished qdiffx linear iterations at : 19:55:54 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 8.2563021E-04 1.7021179E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 19:55:54 12.909u 0.264s 0:13.55 97.1% 0+0k 0+0io 0pf+0w