Tue Oct 11 03:27:11 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 Tue Oct 11 2011 at 03:27:12 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 !!! WARNING: SEP 280 has a net charge of -0.4750 !!! WARNING: HIT 283 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: 0.5657259 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): -13.13600 39.13500 ymin,ymax (A): -24.93400 37.99400 zmin,zma (A): -15.32000 40.08800 x,y,z range (A): 52.27100 62.92800 55.40800 scale (grids/A): 0.5657259 object centre (A): 12.99950 6.530000 12.38400 number of atom coordinates read : 2782 total number of charged atoms : 2633 net assigned charge : 7.539022 assigned positive charge : 430.8436 centred at (gu) : 87.81277 88.33269 89.63308 assigned negative charge : -423.3056 centred at (gu) : 87.74990 88.42703 89.66927 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5766 nv = 96 ne = 84 npr = 55320 no. pairs analyzed = 55320 no. exposed pairs = 3568 no. arc points = 24710 no. surface atoms = 1206 nbur = 1576 mkacc time = 0.1000000 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 = 1.512000 m= 215 mr = 2993 m= 0 mr = 5 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2548 ## 327 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7433 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5683983E-09 4.7275461E-10 midg,1,midg; midg,igrid,midg 3.2422744E-09 -1.4936093E-10 1,midg,midg; igrid,midg,midg 2.4322039E-10 1.0636465E-09 gauss-seidel spectral radius is 0.9838621 estimated iterations to convergence 65 setup time was (sec) 0.4100000 now iterating at: 03:27:12 rms-change max change #iterations 8.6191967E-02 13.70736 at 10iterations 6.4563719E-03 1.063808 at 20iterations 9.7631343E-04 0.1904421 at 30iterations 4.1869190E-04 9.0013504E-02 at 40iterations 2.0300422E-04 4.3679237E-02 at 50iterations finished qdiffx linear iterations at : 03:27:15 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 2.0300422E-04 4.3679237E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 03:27:16 3.467u 0.165s 0:04.08 88.7% 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 Tue Oct 11 2011 at 03:27:16 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 !!! WARNING: SEP 280 has a net charge of -0.4750 !!! WARNING: HIT 283 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: 1.697178 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): -13.13600 39.13500 ymin,ymax (A): -24.93400 37.99400 zmin,zma (A): -15.32000 40.08800 x,y,z range (A): 52.27100 62.92800 55.40800 scale (grids/A): 1.697178 object centre (A): 12.99950 6.530000 12.38400 number of atom coordinates read : 2782 total number of charged atoms : 2633 net assigned charge : 7.539022 assigned positive charge : 430.8436 centred at (gu) : 83.43777 84.99731 88.89847 assigned negative charge : -423.3056 centred at (gu) : 83.24963 85.28109 89.00774 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 63966 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24710 grid for indexing accessible points = 1.400000 m= 19321 mr = 43362 m= 1959 mr = 13181 m= 44 mr = 918 m= 0 mr = 4 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 157 time to turn everything in is 0.3200000 number of dielectric boundary points 27825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20314 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) : 0.5657259 object centre at (A) : 12.99950 6.530000 12.38400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0118286E-02 -6.5125746E-04 midg,1,midg; midg,igrid,midg 2.6164480E-02 -9.3029970E-03 1,midg,midg; igrid,midg,midg 1.4025045E-03 -5.1972405E-05 gauss-seidel spectral radius is 0.9982970 estimated iterations to convergence 192 setup time was (sec) 0.5400000 now iterating at: 03:27:16 rms-change max change #iterations 3.509314 153.8688 at 10iterations 1.504045 61.01654 at 20iterations 0.6452387 26.76442 at 30iterations 0.2772061 10.04791 at 40iterations 0.1187569 5.214300 at 50iterations 5.0878439E-02 2.050770 at 60iterations 2.1892121E-02 0.8152466 at 70iterations 9.4886692E-03 0.3528519 at 80iterations 4.1592810E-03 0.1634521 at 90iterations 1.9579746E-03 8.5844040E-02 at 100iterations 1.0387440E-03 5.0546169E-02 at 110iterations 6.5228052E-04 2.7816772E-02 at 120iterations finished qdiffx linear iterations at : 03:27:24 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 6.5228052E-04 2.7816772E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 03:27:24 7.767u 0.240s 0:08.78 91.1% 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 03:27:25 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 !!! WARNING: SEP 280 has a net charge of -0.4750 !!! WARNING: HIT 283 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: 2.545767 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): -13.13600 39.13500 ymin,ymax (A): -24.93400 37.99400 zmin,zma (A): -15.32000 40.08800 x,y,z range (A): 52.27100 62.92800 55.40800 scale (grids/A): 2.545767 object centre (A): 12.99950 6.530000 12.38400 number of atom coordinates read : 2782 total number of charged atoms : 2633 net assigned charge : 7.539022 assigned positive charge : 430.8436 centred at (gu) : 80.15639 82.49607 88.34764 assigned negative charge : -423.3056 centred at (gu) : 79.87446 82.92152 88.51155 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 148862 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24710 grid for indexing accessible points = 1.400000 m= 67593 mr = 106353 m= 18610 mr = 53236 m= 3034 mr = 13685 m= 224 mr = 2009 m= 2 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 533 time to turn everything in is 0.7900000 number of dielectric boundary points 62931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 21051 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) : 1.697178 object centre at (A) : 12.99950 6.530000 12.38400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4741406E-02 -5.6620101E-03 midg,1,midg; midg,igrid,midg 0.2907437 -0.1266253 1,midg,midg; igrid,midg,midg 3.7783358E-02 -5.5171289E-02 gauss-seidel spectral radius is 0.9991679 estimated iterations to convergence 274 setup time was (sec) 1.040000 now iterating at: 03:27:26 rms-change max change #iterations 8.911515 269.5510 at 10iterations 5.066440 147.3370 at 20iterations 2.875337 72.41873 at 30iterations 1.615105 40.48170 at 40iterations 0.9075606 20.89974 at 50iterations 0.5084091 12.35213 at 60iterations 0.2848644 5.900703 at 70iterations 0.1591780 3.507695 at 80iterations 8.8904418E-02 2.051836 at 90iterations 4.9617596E-02 1.076607 at 100iterations 2.7635388E-02 0.5975742 at 110iterations 1.5482067E-02 0.3410397 at 120iterations 8.7026684E-03 0.1752129 at 130iterations 4.9495548E-03 0.1006994 at 140iterations 2.8854273E-03 6.7810059E-02 at 150iterations 1.7671498E-03 4.6295166E-02 at 160iterations 1.1741816E-03 2.9409409E-02 at 170iterations 8.5323816E-04 2.1862030E-02 at 180iterations finished qdiffx linear iterations at : 03:27:39 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 8.5323816E-04 2.1862030E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 03:27:39 12.492u 0.243s 0:14.74 86.3% 0+0k 0+0io 0pf+0w