Tue Oct 11 08:25:24 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 08:25:24 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2725 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6402302 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): -12.74400 37.04700 ymin,ymax (A): -26.91000 21.57700 zmin,zma (A): -10.01300 45.59200 x,y,z range (A): 49.79100 48.48700 55.60500 scale (grids/A): 0.6402302 object centre (A): 12.15150 -2.666500 17.78950 number of atom coordinates read : 2725 total number of charged atoms : 2598 net assigned charge : 3.162012 assigned positive charge : 416.2368 centred at (gu) : 90.32813 90.50054 91.83944 assigned negative charge : -413.0753 centred at (gu) : 90.08617 90.34638 91.82514 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7518 nv = 96 ne = 84 npr = 53786 no. pairs analyzed = 53786 no. exposed pairs = 3509 no. arc points = 24170 no. surface atoms = 1178 nbur = 1547 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4188 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.3300000 number of dielectric boundary points 3727 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2363 ## 249 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9052 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8382221E-09 9.1454417E-09 midg,1,midg; midg,igrid,midg -1.3518154E-08 2.5955469E-08 1,midg,midg; igrid,midg,midg -2.4667591E-08 3.6248505E-08 gauss-seidel spectral radius is 0.9873715 estimated iterations to convergence 73 setup time was (sec) 0.5900000 now iterating at: 08:25:25 rms-change max change #iterations 0.1504778 20.61311 at 10iterations 1.4980242E-02 2.043224 at 20iterations 1.5399409E-03 0.2193422 at 30iterations 1.6657232E-04 3.0972481E-02 at 40iterations 2.1293456E-05 2.9239655E-03 at 50iterations finished qdiffx linear iterations at : 08:25:29 total time elapsed so far: 4.720000 # loops : 50 mean,max change (kT/e) : 2.1293456E-05 2.9239655E-03 energy calculations done at 4.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.890000 DelPhi exited at 08:25:30 4.897u 0.373s 0:05.98 87.9% 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 08:25:30 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2725 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.920690 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): -12.74400 37.04700 ymin,ymax (A): -26.91000 21.57700 zmin,zma (A): -10.01300 45.59200 x,y,z range (A): 49.79100 48.48700 55.60500 scale (grids/A): 1.920690 object centre (A): 12.15150 -2.666500 17.78950 number of atom coordinates read : 2725 total number of charged atoms : 2598 net assigned charge : 3.162012 assigned positive charge : 416.2368 centred at (gu) : 90.98387 91.50123 95.51768 assigned negative charge : -413.0753 centred at (gu) : 90.25818 91.03873 95.47502 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 80514 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24170 grid for indexing accessible points = 1.400000 m= 29611 mr = 55796 m= 4614 mr = 21773 m= 259 mr = 2764 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 327 time to turn everything in is 0.6600000 number of dielectric boundary points 34577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 20470 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) : 0.6402302 object centre at (A) : 12.15150 -2.666500 17.78950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0850667E-02 3.4003204E-03 midg,1,midg; midg,igrid,midg -1.7950945E-02 6.8789679E-03 1,midg,midg; igrid,midg,midg -6.0983784E-03 6.1693754E-02 gauss-seidel spectral radius is 0.9986745 estimated iterations to convergence 218 setup time was (sec) 0.9600000 now iterating at: 08:25:31 rms-change max change #iterations 4.476714 196.5949 at 10iterations 2.119907 71.50743 at 20iterations 1.005937 30.15690 at 30iterations 0.4774535 15.53516 at 40iterations 0.2261918 6.859600 at 50iterations 0.1073611 3.755256 at 60iterations 5.1052772E-02 1.614830 at 70iterations 2.4224162E-02 0.7315979 at 80iterations 1.1440630E-02 0.3459854 at 90iterations 5.4395096E-03 0.1608152 at 100iterations 2.5803088E-03 8.5044861E-02 at 110iterations 1.2238737E-03 3.5754204E-02 at 120iterations finished qdiffx linear iterations at : 08:25:42 total time elapsed so far: 11.63000 # loops : 120 mean,max change (kT/e) : 1.2238737E-03 3.5754204E-02 energy calculations done at 11.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 08:25:43 11.792u 0.451s 0:12.63 96.9% 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 08:25:43 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2725 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.881036 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): -12.74400 37.04700 ymin,ymax (A): -26.91000 21.57700 zmin,zma (A): -10.01300 45.59200 x,y,z range (A): 49.79100 48.48700 55.60500 scale (grids/A): 2.881036 object centre (A): 12.15150 -2.666500 17.78950 number of atom coordinates read : 2725 total number of charged atoms : 2598 net assigned charge : 3.162012 assigned positive charge : 416.2368 centred at (gu) : 91.47575 92.25173 98.27631 assigned negative charge : -413.0753 centred at (gu) : 90.38726 91.55795 98.21249 start vw surface at 0.1200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 185955 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24170 grid for indexing accessible points = 1.400000 m= 95625 mr = 134968 m= 34507 mr = 78291 m= 8148 mr = 27418 m= 1175 mr = 5977 m= 88 mr = 776 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 1297 time to turn everything in is 1.740000 number of dielectric boundary points 78017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 20784 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) : 1.920690 object centre at (A) : 12.15150 -2.666500 17.78950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3135882 0.1551831 midg,1,midg; midg,igrid,midg -0.2111297 -3.2346450E-02 1,midg,midg; igrid,midg,midg -3.2504924E-02 0.5267572 gauss-seidel spectral radius is 0.9992710 estimated iterations to convergence 292 setup time was (sec) 2.090000 now iterating at: 08:25:45 rms-change max change #iterations 10.46990 338.3425 at 10iterations 6.162356 141.7244 at 20iterations 3.613287 72.96808 at 30iterations 2.111679 43.91827 at 40iterations 1.231998 25.11617 at 50iterations 0.7159924 13.78767 at 60iterations 0.4160884 7.615013 at 70iterations 0.2416520 4.586515 at 80iterations 0.1400899 2.748852 at 90iterations 8.1383914E-02 1.407135 at 100iterations 4.6993338E-02 0.8326044 at 110iterations 2.7220095E-02 0.4636478 at 120iterations 1.5755117E-02 0.2952962 at 130iterations 9.1412570E-03 0.1654387 at 140iterations 5.2981121E-03 9.7709656E-02 at 150iterations 3.0800528E-03 5.7418823E-02 at 160iterations 1.7945892E-03 2.9709816E-02 at 170iterations 1.0528301E-03 1.9063950E-02 at 180iterations finished qdiffx linear iterations at : 08:26:04 total time elapsed so far: 20.27000 # loops : 180 mean,max change (kT/e) : 1.0528301E-03 1.9063950E-02 energy calculations done at 20.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.43000 DelPhi exited at 08:26:04 20.439u 0.458s 0:21.24 98.3% 0+0k 0+0io 0pf+0w