Tue Oct 11 05:51:40 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 05:51:40 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2330 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: 0.7077394 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): 25.63300 72.12100 ymin,ymax (A): -18.71800 31.58300 zmin,zma (A): 3.957000 46.35300 x,y,z range (A): 46.48800 50.30100 42.39600 scale (grids/A): 0.7077394 object centre (A): 48.87700 6.432500 25.15500 number of atom coordinates read : 2330 total number of charged atoms : 2005 net assigned charge : 6.500009 assigned positive charge : 326.1308 centred at (gu) : 89.31619 90.23307 90.34814 assigned negative charge : -319.6311 centred at (gu) : 89.44488 90.18410 90.43156 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7264 nv = 96 ne = 84 npr = 42811 no. pairs analyzed = 42811 no. exposed pairs = 2609 no. arc points = 17680 no. surface atoms = 892 nbur = 1438 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 481 mr = 4208 m= 3 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1616 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7990 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0783956E-08 1.2596627E-08 midg,1,midg; midg,igrid,midg 2.8577920E-08 8.3378580E-08 1,midg,midg; igrid,midg,midg 1.3673854E-07 -9.7228616E-09 gauss-seidel spectral radius is 0.9895964 estimated iterations to convergence 80 setup time was (sec) 0.5600000 now iterating at: 05:51:41 rms-change max change #iterations 0.2011389 27.84970 at 10iterations 2.5235441E-02 3.454628 at 20iterations 3.3166923E-03 0.4154968 at 30iterations 5.6263997E-04 7.8773499E-02 at 40iterations 1.4731068E-04 1.7983437E-02 at 50iterations finished qdiffx linear iterations at : 05:51:44 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 1.4731068E-04 1.7983437E-02 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 05:51:46 4.085u 0.298s 0:06.14 71.1% 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 05:51:46 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2330 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: 2.123218 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): 25.63300 72.12100 ymin,ymax (A): -18.71800 31.58300 zmin,zma (A): 3.957000 46.35300 x,y,z range (A): 46.48800 50.30100 42.39600 scale (grids/A): 2.123218 object centre (A): 48.87700 6.432500 25.15500 number of atom coordinates read : 2330 total number of charged atoms : 2005 net assigned charge : 6.500009 assigned positive charge : 326.1308 centred at (gu) : 87.94839 90.69893 91.04420 assigned negative charge : -319.6311 centred at (gu) : 88.33469 90.55237 91.29478 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76695 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17680 grid for indexing accessible points = 1.400000 m= 31489 mr = 54750 m= 6095 mr = 23985 m= 555 mr = 4087 m= 18 mr = 264 m= 0 mr = 9 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 31757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15902 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) : 0.7077394 object centre at (A) : 48.87700 6.432500 25.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2928800E-02 3.0297088E-02 midg,1,midg; midg,igrid,midg 4.7625013E-02 2.7119962E-02 1,midg,midg; igrid,midg,midg 4.4001754E-02 -4.7333311E-02 gauss-seidel spectral radius is 0.9988360 estimated iterations to convergence 232 setup time was (sec) 1.000000 now iterating at: 05:51:48 rms-change max change #iterations 4.654413 218.1635 at 10iterations 2.307485 78.15018 at 20iterations 1.147767 35.97443 at 30iterations 0.5703390 16.12604 at 40iterations 0.2840514 8.297961 at 50iterations 0.1412026 4.273659 at 60iterations 7.0236586E-02 2.142689 at 70iterations 3.4896009E-02 1.071610 at 80iterations 1.7491532E-02 0.5521965 at 90iterations 8.7630069E-03 0.2610340 at 100iterations 4.4100727E-03 0.1335068 at 110iterations 2.2796229E-03 6.5738201E-02 at 120iterations finished qdiffx linear iterations at : 05:51:56 total time elapsed so far: 9.460000 # loops : 120 mean,max change (kT/e) : 2.2796229E-03 6.5738201E-02 energy calculations done at 9.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.640000 DelPhi exited at 05:51:57 9.644u 0.330s 0:10.45 95.4% 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 05:51:57 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2330 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: 3.184827 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): 25.63300 72.12100 ymin,ymax (A): -18.71800 31.58300 zmin,zma (A): 3.957000 46.35300 x,y,z range (A): 46.48800 50.30100 42.39600 scale (grids/A): 3.184827 object centre (A): 48.87700 6.432500 25.15500 number of atom coordinates read : 2330 total number of charged atoms : 2005 net assigned charge : 6.500009 assigned positive charge : 326.1308 centred at (gu) : 86.92253 91.04850 91.56627 assigned negative charge : -319.6311 centred at (gu) : 87.50195 90.82861 91.94209 start vw surface at 0.1400000 fill in re-entrant regions at 0.9900000 boundary points on vw surface= 176481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17680 grid for indexing accessible points = 1.400000 m= 97405 mr = 131636 m= 40288 mr = 81327 m= 11602 mr = 33055 m= 2279 mr = 9011 m= 267 mr = 1633 m= 14 mr = 166 m= 0 mr = 2 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.290000 number of dielectric boundary points 71506 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.450000 number of grid points assigned charge 16040 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) : 2.123218 object centre at (A) : 48.87700 6.432500 25.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1498508 0.2547861 midg,1,midg; midg,igrid,midg 0.3678259 0.1154998 1,midg,midg; igrid,midg,midg 0.4268028 -0.6004173 gauss-seidel spectral radius is 0.9992989 estimated iterations to convergence 298 setup time was (sec) 2.630000 now iterating at: 05:52:00 rms-change max change #iterations 10.38846 369.8244 at 10iterations 6.158427 170.5250 at 20iterations 3.644535 76.40204 at 30iterations 2.153619 38.48725 at 40iterations 1.266518 23.43642 at 50iterations 0.7457352 15.11351 at 60iterations 0.4383138 8.335765 at 70iterations 0.2574638 5.169991 at 80iterations 0.1510101 3.166307 at 90iterations 8.8771619E-02 1.671387 at 100iterations 5.2133787E-02 0.9373655 at 110iterations 3.0678973E-02 0.5222530 at 120iterations 1.8156592E-02 0.3166728 at 130iterations 1.0857264E-02 0.1974277 at 140iterations 6.6046268E-03 0.1248899 at 150iterations 4.1230237E-03 7.9746246E-02 at 160iterations 2.7034951E-03 5.2513123E-02 at 170iterations 1.8716266E-03 3.6731720E-02 at 180iterations finished qdiffx linear iterations at : 05:52:14 total time elapsed so far: 16.62000 # loops : 180 mean,max change (kT/e) : 1.8716266E-03 3.6731720E-02 energy calculations done at 16.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.81000 DelPhi exited at 05:52:14 16.809u 0.317s 0:17.71 96.6% 0+0k 0+0io 0pf+0w