Sat Oct 8 23:55:54 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+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 Sat Oct 8 2011 at 23:55:54 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.5935609 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): -27.55400 27.71100 ymin,ymax (A): 8.681000 52.28400 zmin,zma (A): -12.46400 47.51300 x,y,z range (A): 55.26500 43.60300 59.97700 scale (grids/A): 0.5935609 object centre (A): 7.8500748E-02 30.48250 17.52450 number of atom coordinates read : 2584 total number of charged atoms : 2448 net assigned charge : 12.51402 assigned positive charge : 380.4839 centred at (gu) : 90.27271 90.21011 90.08418 assigned negative charge : -367.9707 centred at (gu) : 90.28172 90.16209 90.08144 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6009 nv = 96 ne = 84 npr = 51835 no. pairs analyzed = 51835 no. exposed pairs = 3422 no. arc points = 24132 no. surface atoms = 1138 nbur = 1446 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 295 mr = 3039 m= 0 mr = 22 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.2000000 number of dielectric boundary points 3243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2410 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7569 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1810893E-09 4.4977018E-09 midg,1,midg; midg,igrid,midg 2.8386560E-09 5.9636087E-09 1,midg,midg; igrid,midg,midg 4.3220090E-09 4.3358832E-09 gauss-seidel spectral radius is 0.9853171 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 23:55:54 rms-change max change #iterations 0.1017852 17.32534 at 10iterations 8.6542647E-03 1.338554 at 20iterations 1.0784044E-03 0.2219734 at 30iterations 2.7031949E-04 5.9520721E-02 at 40iterations 8.6545821E-05 1.9374847E-02 at 50iterations finished qdiffx linear iterations at : 23:55:57 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 8.6545821E-05 1.9374847E-02 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 23:55:58 3.635u 0.219s 0:04.16 92.3% 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 23:55:58 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.780683 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): -27.55400 27.71100 ymin,ymax (A): 8.681000 52.28400 zmin,zma (A): -12.46400 47.51300 x,y,z range (A): 55.26500 43.60300 59.97700 scale (grids/A): 1.780683 object centre (A): 7.8500748E-02 30.48250 17.52450 number of atom coordinates read : 2584 total number of charged atoms : 2448 net assigned charge : 12.51402 assigned positive charge : 380.4839 centred at (gu) : 90.81770 90.62991 90.25184 assigned negative charge : -367.9707 centred at (gu) : 90.84504 90.48601 90.24427 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66239 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24132 grid for indexing accessible points = 1.400000 m= 21924 mr = 44344 m= 2950 mr = 15286 m= 145 mr = 1644 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2267 time to turn everything in is 0.3500000 number of dielectric boundary points 29943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 215 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19074 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) : 0.5935609 object centre at (A) : 7.8500748E-02 30.48250 17.52450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3743057E-02 1.6299987E-02 midg,1,midg; midg,igrid,midg 4.0674168E-03 1.8410113E-02 1,midg,midg; igrid,midg,midg 2.7105324E-02 3.1327851E-02 gauss-seidel spectral radius is 0.9984510 estimated iterations to convergence 202 setup time was (sec) 0.5800000 now iterating at: 23:55:59 rms-change max change #iterations 3.672610 168.8403 at 10iterations 1.630030 65.62619 at 20iterations 0.7250507 26.98359 at 30iterations 0.3231195 11.64822 at 40iterations 0.1437570 5.636963 at 50iterations 6.4096212E-02 2.400616 at 60iterations 2.8505426E-02 0.9514465 at 70iterations 1.2820026E-02 0.4255514 at 80iterations 5.7924688E-03 0.2016335 at 90iterations 2.6508309E-03 9.0769768E-02 at 100iterations 1.2721004E-03 4.5715332E-02 at 110iterations 6.4902724E-04 2.8964996E-02 at 120iterations finished qdiffx linear iterations at : 23:56:06 total time elapsed so far: 8.310000 # loops : 120 mean,max change (kT/e) : 6.4902724E-04 2.8964996E-02 energy calculations done at 8.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 23:56:07 8.455u 0.226s 0:09.00 96.3% 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 23:56:07 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.671024 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): -27.55400 27.71100 ymin,ymax (A): 8.681000 52.28400 zmin,zma (A): -12.46400 47.51300 x,y,z range (A): 55.26500 43.60300 59.97700 scale (grids/A): 2.671024 object centre (A): 7.8500748E-02 30.48250 17.52450 number of atom coordinates read : 2584 total number of charged atoms : 2448 net assigned charge : 12.51402 assigned positive charge : 380.4839 centred at (gu) : 91.22643 90.94482 90.37749 assigned negative charge : -367.9707 centred at (gu) : 91.26740 90.72900 90.36645 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 153608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24132 grid for indexing accessible points = 1.400000 m= 72625 mr = 108259 m= 23781 mr = 57606 m= 5010 mr = 18370 m= 614 mr = 3474 m= 31 mr = 367 m= 0 mr = 6 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 7441 time to turn everything in is 0.8400000 number of dielectric boundary points 67587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 19578 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) : 1.780683 object centre at (A) : 7.8500748E-02 30.48250 17.52450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5707057 0.3268766 midg,1,midg; midg,igrid,midg 2.2924511E-02 0.2127838 1,midg,midg; igrid,midg,midg 0.3086224 0.3531672 gauss-seidel spectral radius is 0.9992122 estimated iterations to convergence 281 setup time was (sec) 1.100000 now iterating at: 23:56:08 rms-change max change #iterations 9.005980 296.6979 at 10iterations 5.219545 136.1918 at 20iterations 3.002163 64.11130 at 30iterations 1.719515 37.65997 at 40iterations 0.9819185 20.43180 at 50iterations 0.5598581 12.11877 at 60iterations 0.3184043 6.259794 at 70iterations 0.1807266 4.024315 at 80iterations 0.1025701 2.198607 at 90iterations 5.8014747E-02 1.235048 at 100iterations 3.2839771E-02 0.6368175 at 110iterations 1.8548932E-02 0.3713961 at 120iterations 1.0516044E-02 0.2336760 at 130iterations 5.9455223E-03 0.1283646 at 140iterations 3.3662403E-03 6.8019867E-02 at 150iterations 1.9007948E-03 3.7658691E-02 at 160iterations 1.0779836E-03 2.1858215E-02 at 170iterations 6.1209314E-04 1.2491226E-02 at 180iterations finished qdiffx linear iterations at : 23:56:20 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 6.1209314E-04 1.2491226E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.28000 DelPhi exited at 23:56:21 13.281u 0.231s 0:13.78 98.0% 0+0k 0+0io 0pf+0w