Tue Oct 11 03:23:38 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 Tue Oct 11 2011 at 03:23:38 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1184 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7205895 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): -6.908000 31.91200 ymin,ymax (A): 1.116000 39.54100 zmin,zma (A): -3.252000 46.15200 x,y,z range (A): 38.82000 38.42500 49.40400 scale (grids/A): 0.7205895 object centre (A): 12.50200 20.32850 21.45000 number of atom coordinates read : 1184 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 88.76235 89.35374 89.03500 assigned negative charge : -169.8232 centred at (gu) : 88.44037 89.31821 89.07229 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4168 nv = 96 ne = 84 npr = 23409 no. pairs analyzed = 23409 no. exposed pairs = 1495 no. arc points = 10973 no. surface atoms = 504 nbur = 680 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 235 mr = 2126 m= 0 mr = 40 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 46 time to turn everything in is 0.1200000 number of dielectric boundary points 2237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 941 ## 87 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4328 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3349392E-08 4.2985064E-08 midg,1,midg; midg,igrid,midg 5.8313695E-08 6.8483054E-08 1,midg,midg; igrid,midg,midg -7.0696593E-08 1.3916411E-07 gauss-seidel spectral radius is 0.9898741 estimated iterations to convergence 81 setup time was (sec) 0.3000000 now iterating at: 03:23:38 rms-change max change #iterations 0.1564416 30.98624 at 10iterations 2.0195721E-02 3.510250 at 20iterations 2.4828161E-03 0.4747086 at 30iterations 3.1784683E-04 5.9471130E-02 at 40iterations 3.9267616E-05 7.8182220E-03 at 50iterations finished qdiffx linear iterations at : 03:23:41 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 3.9267616E-05 7.8182220E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 03:23:42 3.310u 0.169s 0:03.80 91.3% 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 Tue Oct 11 2011 at 03:23:42 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1184 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.161768 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): -6.908000 31.91200 ymin,ymax (A): 1.116000 39.54100 zmin,zma (A): -3.252000 46.15200 x,y,z range (A): 38.82000 38.42500 49.40400 scale (grids/A): 2.161768 object centre (A): 12.50200 20.32850 21.45000 number of atom coordinates read : 1184 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 86.28712 88.06126 87.10509 assigned negative charge : -169.8232 centred at (gu) : 85.32121 87.95492 87.21702 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 43574 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10973 grid for indexing accessible points = 1.400000 m= 16067 mr = 28484 m= 3028 mr = 11926 m= 289 mr = 1995 m= 16 mr = 162 m= 0 mr = 12 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 1348 time to turn everything in is 0.2400000 number of dielectric boundary points 20395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8433 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) : 0.7205895 object centre at (A) : 12.50200 20.32850 21.45000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9101261E-03 2.1979911E-03 midg,1,midg; midg,igrid,midg 2.8499767E-02 2.7326869E-02 1,midg,midg; igrid,midg,midg -2.7533319E-02 3.4952059E-02 gauss-seidel spectral radius is 0.9987811 estimated iterations to convergence 227 setup time was (sec) 0.4600000 now iterating at: 03:23:42 rms-change max change #iterations 3.461314 194.4062 at 10iterations 1.694027 82.59309 at 20iterations 0.8194917 32.24310 at 30iterations 0.3993787 15.78041 at 40iterations 0.1952338 8.373898 at 50iterations 9.4723284E-02 3.821674 at 60iterations 4.6100046E-02 1.811937 at 70iterations 2.2466291E-02 0.9472008 at 80iterations 1.0930230E-02 0.4038811 at 90iterations 5.3334055E-03 0.1961961 at 100iterations 2.5988873E-03 0.1133804 at 110iterations 1.2694976E-03 4.8942566E-02 at 120iterations finished qdiffx linear iterations at : 03:23:49 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 1.2694976E-03 4.8942566E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 03:23:50 7.639u 0.199s 0:08.13 96.1% 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 03:23:50 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1184 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.242652 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): -6.908000 31.91200 ymin,ymax (A): 1.116000 39.54100 zmin,zma (A): -3.252000 46.15200 x,y,z range (A): 38.82000 38.42500 49.40400 scale (grids/A): 3.242652 object centre (A): 12.50200 20.32850 21.45000 number of atom coordinates read : 1184 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 84.43073 87.09193 85.65772 assigned negative charge : -169.8232 centred at (gu) : 82.98181 86.93244 85.82560 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 100265 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10973 grid for indexing accessible points = 1.400000 m= 50066 mr = 68740 m= 20027 mr = 40781 m= 5696 mr = 16400 m= 1164 mr = 4487 m= 152 mr = 879 m= 12 mr = 108 m= 0 mr = 12 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 4570 time to turn everything in is 0.6700000 number of dielectric boundary points 45975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 8488 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) : 2.161768 object centre at (A) : 12.50200 20.32850 21.45000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6591325E-02 8.8399462E-03 midg,1,midg; midg,igrid,midg 0.2582441 0.2312575 1,midg,midg; igrid,midg,midg -0.2440979 0.2670099 gauss-seidel spectral radius is 0.9992760 estimated iterations to convergence 293 setup time was (sec) 0.8900000 now iterating at: 03:23:51 rms-change max change #iterations 7.604180 269.0647 at 10iterations 4.385529 109.1824 at 20iterations 2.524621 54.02751 at 30iterations 1.454645 33.44822 at 40iterations 0.8357102 20.05477 at 50iterations 0.4808429 10.43798 at 60iterations 0.2773364 6.028101 at 70iterations 0.1595331 3.388031 at 80iterations 9.1732331E-02 1.874477 at 90iterations 5.2849527E-02 1.164360 at 100iterations 3.0495619E-02 0.6514649 at 110iterations 1.7533027E-02 0.4152222 at 120iterations 1.0119609E-02 0.2186832 at 130iterations 5.8105597E-03 0.1292496 at 140iterations 3.3573278E-03 7.1015358E-02 at 150iterations 1.9339430E-03 4.8207670E-02 at 160iterations 1.1094408E-03 2.6981354E-02 at 170iterations 6.4220378E-04 1.3572693E-02 at 180iterations finished qdiffx linear iterations at : 03:24:02 total time elapsed so far: 11.67000 # loops : 180 mean,max change (kT/e) : 6.4220378E-04 1.3572693E-02 energy calculations done at 11.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.80000 DelPhi exited at 03:24:02 11.800u 0.209s 0:12.43 96.5% 0+0k 0+0io 0pf+0w