Mon Oct 10 19:34:38 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 19:34:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2691 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: 0.5597220 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): -8.143001 38.01800 ymin,ymax (A): -9.147000 41.70600 zmin,zma (A): -1.282000 62.32100 x,y,z range (A): 46.16100 50.85300 63.60300 scale (grids/A): 0.5597220 object centre (A): 14.93750 16.27950 30.51950 number of atom coordinates read : 2691 total number of charged atoms : 2550 net assigned charge : 3.000025 assigned positive charge : 396.1759 centred at (gu) : 90.67890 89.29456 89.27650 assigned negative charge : -393.1767 centred at (gu) : 90.59370 89.23952 89.38364 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5572 nv = 96 ne = 84 npr = 53632 no. pairs analyzed = 53632 no. exposed pairs = 3549 no. arc points = 24720 no. surface atoms = 1195 nbur = 1496 mkacc time = 0.1200000 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 = 1.540000 m= 231 mr = 2806 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2504 ## 329 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7156 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5887713E-09 -6.2292010E-10 midg,1,midg; midg,igrid,midg -2.7849409E-10 7.0547457E-10 1,midg,midg; igrid,midg,midg -4.4548046E-10 1.3257736E-09 gauss-seidel spectral radius is 0.9835160 estimated iterations to convergence 64 setup time was (sec) 0.5100000 now iterating at: 19:34:39 rms-change max change #iterations 7.5351037E-02 14.25226 at 10iterations 5.2698180E-03 0.8698330 at 20iterations 3.8182150E-04 6.4249992E-02 at 30iterations 2.7266535E-05 4.6305656E-03 at 40iterations 2.0983912E-06 3.6430359E-04 at 50iterations finished qdiffx linear iterations at : 19:34:42 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 2.0983912E-06 3.6430359E-04 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 19:34:42 3.281u 0.191s 0:03.84 90.3% 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 Mon Oct 10 2011 at 19:34:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2691 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: 1.679166 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): -8.143001 38.01800 ymin,ymax (A): -9.147000 41.70600 zmin,zma (A): -1.282000 62.32100 x,y,z range (A): 46.16100 50.85300 63.60300 scale (grids/A): 1.679166 object centre (A): 14.93750 16.27950 30.51950 number of atom coordinates read : 2691 total number of charged atoms : 2550 net assigned charge : 3.000025 assigned positive charge : 396.1759 centred at (gu) : 92.03651 87.88328 87.82912 assigned negative charge : -393.1767 centred at (gu) : 91.78108 87.71854 88.15067 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 61153 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24720 grid for indexing accessible points = 1.400000 m= 19369 mr = 40702 m= 2200 mr = 13294 m= 73 mr = 1116 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 413 time to turn everything in is 0.4400000 number of dielectric boundary points 27676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 245 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 19665 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) : 0.5597220 object centre at (A) : 14.93750 16.27950 30.51950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2375589E-02 1.0897062E-02 midg,1,midg; midg,igrid,midg -8.6122453E-03 -2.4854550E-03 1,midg,midg; igrid,midg,midg -2.0161010E-03 2.8271610E-03 gauss-seidel spectral radius is 0.9982611 estimated iterations to convergence 190 setup time was (sec) 0.7300000 now iterating at: 19:34:43 rms-change max change #iterations 3.296070 166.2827 at 10iterations 1.390208 55.86210 at 20iterations 0.5893090 22.42466 at 30iterations 0.2498414 9.154383 at 40iterations 0.1055701 3.869131 at 50iterations 4.5082808E-02 1.661900 at 60iterations 1.9121613E-02 0.7153683 at 70iterations 8.1119742E-03 0.2961979 at 80iterations 3.4429345E-03 0.1274753 at 90iterations 1.4642929E-03 5.3081512E-02 at 100iterations 6.2157807E-04 2.2308350E-02 at 110iterations 2.6484995E-04 9.1221333E-03 at 120iterations finished qdiffx linear iterations at : 19:34:49 total time elapsed so far: 7.140000 # loops : 120 mean,max change (kT/e) : 2.6484995E-04 9.1221333E-03 energy calculations done at 7.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.320000 DelPhi exited at 19:34:50 7.320u 0.203s 0:08.03 93.6% 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 Mon Oct 10 2011 at 19:34:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2691 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: 2.518749 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): -8.143001 38.01800 ymin,ymax (A): -9.147000 41.70600 zmin,zma (A): -1.282000 62.32100 x,y,z range (A): 46.16100 50.85300 63.60300 scale (grids/A): 2.518749 object centre (A): 14.93750 16.27950 30.51950 number of atom coordinates read : 2691 total number of charged atoms : 2550 net assigned charge : 3.000025 assigned positive charge : 396.1759 centred at (gu) : 93.05447 86.82479 86.74352 assigned negative charge : -393.1767 centred at (gu) : 92.67158 86.57780 87.22597 start vw surface at 0.1500000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 141757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24720 grid for indexing accessible points = 1.400000 m= 65811 mr = 99550 m= 19936 mr = 51820 m= 3663 mr = 15067 m= 319 mr = 2408 m= 6 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 1292 time to turn everything in is 1.070000 number of dielectric boundary points 62498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 20387 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) : 1.679166 object centre at (A) : 14.93750 16.27950 30.51950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3849938 0.3140969 midg,1,midg; midg,igrid,midg -7.2026879E-02 -5.3127367E-02 1,midg,midg; igrid,midg,midg -3.5169497E-02 2.8402083E-02 gauss-seidel spectral radius is 0.9991612 estimated iterations to convergence 273 setup time was (sec) 1.370000 now iterating at: 19:34:52 rms-change max change #iterations 8.465274 353.9083 at 10iterations 4.780246 136.9530 at 20iterations 2.681270 90.65844 at 30iterations 1.501222 35.46521 at 40iterations 0.8362253 20.47784 at 50iterations 0.4661461 10.60868 at 60iterations 0.2592264 7.374966 at 70iterations 0.1437768 3.028660 at 80iterations 7.9608358E-02 1.735428 at 90iterations 4.4101711E-02 0.9740982 at 100iterations 2.4473708E-02 0.4982033 at 110iterations 1.3539420E-02 0.2735901 at 120iterations 7.4913376E-03 0.1517639 at 130iterations 4.1449098E-03 8.8955760E-02 at 140iterations 2.2956892E-03 4.7206879E-02 at 150iterations 1.2708595E-03 2.5914192E-02 at 160iterations 7.0251309E-04 1.5144348E-02 at 170iterations 3.8930454E-04 8.9302063E-03 at 180iterations finished qdiffx linear iterations at : 19:35:02 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 3.8930454E-04 8.9302063E-03 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 19:35:03 11.796u 0.234s 0:12.36 97.2% 0+0k 0+0io 0pf+0w