Sat Oct 15 12:01:58 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 15 2011 at 12:01:58 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 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: 0.6447757 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): 6.369000 61.58200 ymin,ymax (A): -9.665000 33.70500 zmin,zma (A): -14.20300 41.00600 x,y,z range (A): 55.21300 43.37000 55.20900 scale (grids/A): 0.6447757 object centre (A): 33.97550 12.02000 13.40150 number of atom coordinates read : 2298 total number of charged atoms : 2164 net assigned charge : 9.000025 assigned positive charge : 334.4816 centred at (gu) : 90.78741 91.02158 89.37004 assigned negative charge : -325.4822 centred at (gu) : 90.80911 90.90074 89.40221 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6520 nv = 96 ne = 84 npr = 45886 no. pairs analyzed = 45886 no. exposed pairs = 3116 no. arc points = 21839 no. surface atoms = 1042 nbur = 1256 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 3301 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 7.9999991E-02 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.1900000 number of dielectric boundary points 3567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2180 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7734 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0976698E-08 9.9142010E-09 midg,1,midg; midg,igrid,midg 1.1315554E-09 3.4881161E-08 1,midg,midg; igrid,midg,midg 1.4665450E-08 1.4577727E-08 gauss-seidel spectral radius is 0.9875200 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 12:01:58 rms-change max change #iterations 0.1384473 21.37847 at 10iterations 1.4053704E-02 1.885098 at 20iterations 1.3941218E-03 0.2112141 at 30iterations 1.4344619E-04 2.5042534E-02 at 40iterations 1.4721501E-05 1.9912720E-03 at 50iterations finished qdiffx linear iterations at : 12:02:01 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.4721501E-05 1.9912720E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 12:02:02 3.459u 0.198s 0:03.97 91.6% 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 15 2011 at 12:02:02 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 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: 1.934327 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): 6.369000 61.58200 ymin,ymax (A): -9.665000 33.70500 zmin,zma (A): -14.20300 41.00600 x,y,z range (A): 55.21300 43.37000 55.20900 scale (grids/A): 1.934327 object centre (A): 33.97550 12.02000 13.40150 number of atom coordinates read : 2298 total number of charged atoms : 2164 net assigned charge : 9.000025 assigned positive charge : 334.4816 centred at (gu) : 92.36203 93.06458 88.10972 assigned negative charge : -325.4822 centred at (gu) : 92.42757 92.70232 88.20673 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 70084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21839 grid for indexing accessible points = 1.400000 m= 25019 mr = 46386 m= 4362 mr = 17774 m= 362 mr = 2685 m= 6 mr = 143 m= 0 mr = 3 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 345 time to turn everything in is 0.3500000 number of dielectric boundary points 32842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17057 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) : 0.6447757 object centre at (A) : 33.97550 12.02000 13.40150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6953831E-02 4.0357165E-02 midg,1,midg; midg,igrid,midg -6.8432745E-03 3.2701697E-02 1,midg,midg; igrid,midg,midg 4.8200034E-02 3.5690431E-02 gauss-seidel spectral radius is 0.9986545 estimated iterations to convergence 216 setup time was (sec) 0.5800000 now iterating at: 12:02:03 rms-change max change #iterations 4.022356 201.6849 at 10iterations 1.890122 69.20155 at 20iterations 0.8888605 33.70554 at 30iterations 0.4171314 13.86256 at 40iterations 0.1961330 6.276375 at 50iterations 9.1829643E-02 3.038819 at 60iterations 4.3209147E-02 1.502893 at 70iterations 2.0361247E-02 0.6582391 at 80iterations 9.5637217E-03 0.3164959 at 90iterations 4.4954037E-03 0.1530628 at 100iterations 2.1176534E-03 6.4876556E-02 at 110iterations 9.9529559E-04 3.0853271E-02 at 120iterations finished qdiffx linear iterations at : 12:02:10 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 9.9529559E-04 3.0853271E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 12:02:11 7.986u 0.258s 0:08.68 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 15 2011 at 12:02:11 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 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: 2.901491 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): 6.369000 61.58200 ymin,ymax (A): -9.665000 33.70500 zmin,zma (A): -14.20300 41.00600 x,y,z range (A): 55.21300 43.37000 55.20900 scale (grids/A): 2.901491 object centre (A): 33.97550 12.02000 13.40150 number of atom coordinates read : 2298 total number of charged atoms : 2164 net assigned charge : 9.000025 assigned positive charge : 334.4816 centred at (gu) : 93.54311 94.59676 87.16460 assigned negative charge : -325.4822 centred at (gu) : 93.64149 94.05360 87.31007 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 161975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21839 grid for indexing accessible points = 1.400000 m= 79740 mr = 113070 m= 29803 mr = 63492 m= 7888 mr = 23454 m= 1492 mr = 5810 m= 138 mr = 1050 m= 7 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 1306 time to turn everything in is 0.9200000 number of dielectric boundary points 74075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 17311 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) : 1.934327 object centre at (A) : 33.97550 12.02000 13.40150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4203773 0.4090255 midg,1,midg; midg,igrid,midg -6.6030383E-02 0.3303026 1,midg,midg; igrid,midg,midg 0.6803737 0.4054405 gauss-seidel spectral radius is 0.9992710 estimated iterations to convergence 292 setup time was (sec) 1.180000 now iterating at: 12:02:12 rms-change max change #iterations 9.505065 340.5476 at 10iterations 5.640220 132.4751 at 20iterations 3.303365 78.47740 at 30iterations 1.938788 41.24808 at 40iterations 1.126746 24.29835 at 50iterations 0.6560744 14.06424 at 60iterations 0.3811274 7.664791 at 70iterations 0.2212133 4.798676 at 80iterations 0.1278044 2.710001 at 90iterations 7.4203506E-02 1.532982 at 100iterations 4.2930260E-02 0.8107538 at 110iterations 2.4849774E-02 0.5151031 at 120iterations 1.4299653E-02 0.2691796 at 130iterations 8.2720937E-03 0.1532669 at 140iterations 4.7774743E-03 8.4975004E-02 at 150iterations 2.7622427E-03 5.0632477E-02 at 160iterations 1.5884946E-03 2.9282570E-02 at 170iterations 9.1745146E-04 1.6269684E-02 at 180iterations finished qdiffx linear iterations at : 12:02:24 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 9.1745146E-04 1.6269684E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 12:02:24 13.046u 0.235s 0:13.66 97.1% 0+0k 0+0io 0pf+0w