Tue Oct 11 08:33:02 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 08:33:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.6411642 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): -13.11900 36.89200 ymin,ymax (A): -26.82400 21.65100 zmin,zma (A): -10.21400 45.31000 x,y,z range (A): 50.01100 48.47500 55.52400 scale (grids/A): 0.6411642 object centre (A): 11.88650 -2.586500 17.54800 number of atom coordinates read : 2750 total number of charged atoms : 2602 net assigned charge : 2.500016 assigned positive charge : 416.3686 centred at (gu) : 90.56463 90.43690 91.78643 assigned negative charge : -413.8693 centred at (gu) : 90.33138 90.30950 91.74319 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7470 nv = 96 ne = 84 npr = 55717 no. pairs analyzed = 55717 no. exposed pairs = 3338 no. arc points = 23304 no. surface atoms = 1124 nbur = 1626 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 402 mr = 4210 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2292 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9082 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4026180E-09 1.3116920E-08 midg,1,midg; midg,igrid,midg -1.1907522E-08 2.1431694E-08 1,midg,midg; igrid,midg,midg -2.4038451E-08 3.6767574E-08 gauss-seidel spectral radius is 0.9874075 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 08:33:02 rms-change max change #iterations 0.1521095 19.92769 at 10iterations 1.5377589E-02 2.296497 at 20iterations 1.5644582E-03 0.2254238 at 30iterations 1.7315813E-04 2.1999359E-02 at 40iterations 2.4539086E-05 3.2081604E-03 at 50iterations finished qdiffx linear iterations at : 08:33:05 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.4539086E-05 3.2081604E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 08:33:06 3.407u 0.164s 0:03.85 92.4% 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 08:33:06 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 = 2750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.923492 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): -13.11900 36.89200 ymin,ymax (A): -26.82400 21.65100 zmin,zma (A): -10.21400 45.31000 x,y,z range (A): 50.01100 48.47500 55.52400 scale (grids/A): 1.923492 object centre (A): 11.88650 -2.586500 17.54800 number of atom coordinates read : 2750 total number of charged atoms : 2602 net assigned charge : 2.500016 assigned positive charge : 416.3686 centred at (gu) : 91.69330 91.31021 95.35889 assigned negative charge : -413.8693 centred at (gu) : 90.99380 90.92812 95.22923 start vw surface at 0.2300000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 81138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23304 grid for indexing accessible points = 1.400000 m= 29771 mr = 57242 m= 4864 mr = 22180 m= 334 mr = 3164 m= 7 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 920 time to turn everything in is 0.6300000 number of dielectric boundary points 33388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 182 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20522 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) : 0.6411642 object centre at (A) : 11.88650 -2.586500 17.54800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0062656E-02 2.8556425E-03 midg,1,midg; midg,igrid,midg -1.6124740E-02 7.2313650E-03 1,midg,midg; igrid,midg,midg -1.2687904E-02 6.7702428E-02 gauss-seidel spectral radius is 0.9986765 estimated iterations to convergence 218 setup time was (sec) 0.8900000 now iterating at: 08:33:07 rms-change max change #iterations 4.486811 190.3545 at 10iterations 2.123930 71.72121 at 20iterations 1.007803 30.16739 at 30iterations 0.4795547 17.14091 at 40iterations 0.2273532 7.667591 at 50iterations 0.1083601 3.303493 at 60iterations 5.1355831E-02 1.576816 at 70iterations 2.4361920E-02 0.7512856 at 80iterations 1.1588125E-02 0.3605652 at 90iterations 5.5047576E-03 0.1702728 at 100iterations 2.6143843E-03 7.7917099E-02 at 110iterations 1.2467988E-03 3.8865089E-02 at 120iterations finished qdiffx linear iterations at : 08:33:13 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 1.2467988E-03 3.8865089E-02 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.370000 DelPhi exited at 08:33:14 7.373u 0.174s 0:08.24 91.5% 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 08:33:14 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 = 2750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.885239 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): -13.11900 36.89200 ymin,ymax (A): -26.82400 21.65100 zmin,zma (A): -10.21400 45.31000 x,y,z range (A): 50.01100 48.47500 55.52400 scale (grids/A): 2.885239 object centre (A): 11.88650 -2.586500 17.54800 number of atom coordinates read : 2750 total number of charged atoms : 2602 net assigned charge : 2.500016 assigned positive charge : 416.3686 centred at (gu) : 92.53978 91.96509 98.03812 assigned negative charge : -413.8693 centred at (gu) : 91.49070 91.39216 97.84383 start vw surface at 0.2200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 187733 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23304 grid for indexing accessible points = 1.400000 m= 96119 mr = 138277 m= 35324 mr = 79407 m= 8818 mr = 28702 m= 1360 mr = 6723 m= 110 mr = 959 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 3253 time to turn everything in is 1.640000 number of dielectric boundary points 75343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 20815 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) : 1.923492 object centre at (A) : 11.88650 -2.586500 17.54800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3079810 0.1397468 midg,1,midg; midg,igrid,midg -0.1747331 1.2441350E-02 1,midg,midg; igrid,midg,midg -0.1002454 0.5775717 gauss-seidel spectral radius is 0.9992679 estimated iterations to convergence 292 setup time was (sec) 1.920000 now iterating at: 08:33:16 rms-change max change #iterations 10.36853 397.0282 at 10iterations 6.067027 135.3432 at 20iterations 3.542704 65.88693 at 30iterations 2.062193 43.15740 at 40iterations 1.195271 21.15716 at 50iterations 0.6930853 13.73589 at 60iterations 0.4024214 7.482877 at 70iterations 0.2329599 4.358637 at 80iterations 0.1349595 2.275780 at 90iterations 7.8020141E-02 1.326097 at 100iterations 4.5031499E-02 0.8138359 at 110iterations 2.6136862E-02 0.4468784 at 120iterations 1.5107086E-02 0.2795277 at 130iterations 8.7520918E-03 0.2052498 at 140iterations 5.0679981E-03 9.7480774E-02 at 150iterations 2.9489142E-03 5.1536560E-02 at 160iterations 1.7209586E-03 2.9663086E-02 at 170iterations 1.0132178E-03 1.8273354E-02 at 180iterations finished qdiffx linear iterations at : 08:33:27 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 1.0132178E-03 1.8273354E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 08:33:27 12.608u 0.194s 0:13.34 95.8% 0+0k 0+0io 0pf+0w