Sat Oct 15 12:54:27 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 12:54:28 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 = 3509 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: 0.5256164 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): -15.45400 51.73900 ymin,ymax (A): -26.20100 41.52900 zmin,zma (A): 3.104000 55.53000 x,y,z range (A): 67.19300 67.73000 52.42600 scale (grids/A): 0.5256164 object centre (A): 18.14250 7.664001 29.31700 number of atom coordinates read : 3509 total number of charged atoms : 3362 net assigned charge : 2.000019 assigned positive charge : 521.3888 centred at (gu) : 90.18044 90.10281 91.00009 assigned negative charge : -519.3911 centred at (gu) : 90.18147 90.19688 90.97079 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6606 nv = 96 ne = 84 npr = 66951 no. pairs analyzed = 66951 no. exposed pairs = 5132 no. arc points = 36832 no. surface atoms = 1702 nbur = 1807 mkacc time = 0.1700000 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 = 1.624000 m= 238 mr = 2990 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3516 ## 448 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7867921E-11 2.0257891E-10 midg,1,midg; midg,igrid,midg 3.7079065E-10 -2.8907410E-10 1,midg,midg; igrid,midg,midg 5.4875514E-11 5.2452296E-11 gauss-seidel spectral radius is 0.9814178 estimated iterations to convergence 61 setup time was (sec) 0.6900000 now iterating at: 12:54:29 rms-change max change #iterations 6.4452276E-02 10.31171 at 10iterations 3.8885400E-03 0.7193184 at 20iterations 2.5561335E-04 4.4853210E-02 at 30iterations 2.6463575E-05 6.2942505E-03 at 40iterations 5.0859448E-06 1.2741089E-03 at 50iterations finished qdiffx linear iterations at : 12:54:33 total time elapsed so far: 5.180000 # loops : 50 mean,max change (kT/e) : 5.0859448E-06 1.2741089E-03 energy calculations done at 5.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.350000 DelPhi exited at 12:54:34 5.350u 0.457s 0:06.09 95.2% 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 12:54:34 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 = 3509 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: 1.576849 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): -15.45400 51.73900 ymin,ymax (A): -26.20100 41.52900 zmin,zma (A): 3.104000 55.53000 x,y,z range (A): 67.19300 67.73000 52.42600 scale (grids/A): 1.576849 object centre (A): 18.14250 7.664001 29.31700 number of atom coordinates read : 3509 total number of charged atoms : 3362 net assigned charge : 2.000019 assigned positive charge : 521.3888 centred at (gu) : 90.54034 90.30766 92.99942 assigned negative charge : -519.3911 centred at (gu) : 90.54408 90.59017 92.91200 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72679 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36832 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20975 mr = 45817 m= 2098 mr = 13098 m= 42 mr = 849 m= 0 mr = 1 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.6300000 number of dielectric boundary points 36029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 374 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 25579 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) : 0.5256164 object centre at (A) : 18.14250 7.664001 29.31700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7805939E-03 1.4713162E-04 midg,1,midg; midg,igrid,midg 2.5985690E-02 6.9257310E-03 1,midg,midg; igrid,midg,midg 6.6568382E-04 1.1802371E-02 gauss-seidel spectral radius is 0.9981369 estimated iterations to convergence 184 setup time was (sec) 1.040000 now iterating at: 12:54:35 rms-change max change #iterations 3.395888 169.1957 at 10iterations 1.392014 50.32507 at 20iterations 0.5726801 22.02707 at 30iterations 0.2358781 10.04521 at 40iterations 9.7277105E-02 3.265577 at 50iterations 4.0051993E-02 1.595621 at 60iterations 1.6519174E-02 0.6051540 at 70iterations 6.8043070E-03 0.2372589 at 80iterations 2.8036344E-03 0.1037216 at 90iterations 1.1564075E-03 4.0275574E-02 at 100iterations 4.7826266E-04 1.8306345E-02 at 110iterations 1.9750447E-04 6.6776276E-03 at 120iterations finished qdiffx linear iterations at : 12:54:47 total time elapsed so far: 13.00000 # loops : 120 mean,max change (kT/e) : 1.9750447E-04 6.6776276E-03 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 12:54:48 13.166u 0.510s 0:14.14 96.6% 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 12:54:48 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 = 3509 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: 2.365274 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): -15.45400 51.73900 ymin,ymax (A): -26.20100 41.52900 zmin,zma (A): 3.104000 55.53000 x,y,z range (A): 67.19300 67.73000 52.42600 scale (grids/A): 2.365274 object centre (A): 18.14250 7.664001 29.31700 number of atom coordinates read : 3509 total number of charged atoms : 3362 net assigned charge : 2.000019 assigned positive charge : 521.3888 centred at (gu) : 90.81039 90.46127 94.49863 assigned negative charge : -519.3911 centred at (gu) : 90.81601 90.88503 94.36800 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 169275 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36832 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 72067 mr = 113846 m= 20014 mr = 53359 m= 3007 mr = 13979 m= 155 mr = 1758 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 1.560000 number of dielectric boundary points 81539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 26845 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) : 1.576849 object centre at (A) : 18.14250 7.664001 29.31700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7145164E-02 -7.1931132E-03 midg,1,midg; midg,igrid,midg 0.4875989 -1.8106835E-02 1,midg,midg; igrid,midg,midg 1.7676737E-02 0.3930497 gauss-seidel spectral radius is 0.9991513 estimated iterations to convergence 271 setup time was (sec) 1.960000 now iterating at: 12:54:50 rms-change max change #iterations 9.216879 324.2659 at 10iterations 5.311515 172.5293 at 20iterations 3.027963 77.13836 at 30iterations 1.711050 44.85684 at 40iterations 0.9646363 25.28855 at 50iterations 0.5388606 16.92212 at 60iterations 0.3018231 6.729500 at 70iterations 0.1680136 4.170708 at 80iterations 9.3310721E-02 2.527100 at 90iterations 5.1831931E-02 1.161156 at 100iterations 2.8700540E-02 0.6436882 at 110iterations 1.5883109E-02 0.3335381 at 120iterations 8.7859239E-03 0.1790473 at 130iterations 4.8671686E-03 0.1061974 at 140iterations 2.6965179E-03 5.2996635E-02 at 150iterations 1.4908150E-03 2.9854059E-02 at 160iterations 8.2449109E-04 1.5956879E-02 at 170iterations 4.5585228E-04 9.7477436E-03 at 180iterations finished qdiffx linear iterations at : 12:55:10 total time elapsed so far: 21.38000 # loops : 180 mean,max change (kT/e) : 4.5585228E-04 9.7477436E-03 energy calculations done at 21.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.56000 DelPhi exited at 12:55:10 21.564u 0.556s 0:22.51 98.2% 0+0k 0+0io 0pf+0w