Sat Oct 8 23:50:02 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 Sat Oct 8 2011 at 23:50:02 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 = 2153 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6819531 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): -12.20300 40.00000 ymin,ymax (A): 14.17800 65.91800 zmin,zma (A): 3.129000 45.39300 x,y,z range (A): 52.20300 51.74000 42.26400 scale (grids/A): 0.6819531 object centre (A): 13.89850 40.04800 24.26100 number of atom coordinates read : 2153 total number of charged atoms : 2018 net assigned charge : 9.500023 assigned positive charge : 310.3229 centred at (gu) : 88.98110 88.55515 88.48169 assigned negative charge : -300.8232 centred at (gu) : 89.04095 88.52496 88.58303 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 7061 nv = 96 ne = 84 npr = 42806 no. pairs analyzed = 42806 no. exposed pairs = 2893 no. arc points = 21077 no. surface atoms = 953 nbur = 1200 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 3705 m= 6 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 84 time to turn everything in is 0.1600000 number of dielectric boundary points 3750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1965 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7918 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3018343E-08 1.1768601E-08 midg,1,midg; midg,igrid,midg 4.5266532E-08 3.7843080E-08 1,midg,midg; igrid,midg,midg 7.0834410E-08 2.1821714E-08 gauss-seidel spectral radius is 0.9888225 estimated iterations to convergence 77 setup time was (sec) 0.3600000 now iterating at: 23:50:02 rms-change max change #iterations 0.1681218 23.14379 at 10iterations 1.9478220E-02 2.646185 at 20iterations 2.1791141E-03 0.3144760 at 30iterations 2.5000502E-04 3.2092094E-02 at 40iterations 2.8449382E-05 3.6554337E-03 at 50iterations finished qdiffx linear iterations at : 23:50:05 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.8449382E-05 3.6554337E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 23:50:06 3.426u 0.197s 0:03.91 92.3% 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 Sat Oct 8 2011 at 23:50:06 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 = 2153 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.045860 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): -12.20300 40.00000 ymin,ymax (A): 14.17800 65.91800 zmin,zma (A): 3.129000 45.39300 x,y,z range (A): 52.20300 51.74000 42.26400 scale (grids/A): 2.045860 object centre (A): 13.89850 40.04800 24.26100 number of atom coordinates read : 2153 total number of charged atoms : 2018 net assigned charge : 9.500023 assigned positive charge : 310.3229 centred at (gu) : 86.94309 85.66553 85.44506 assigned negative charge : -300.8232 centred at (gu) : 87.12294 85.57497 85.74905 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21077 grid for indexing accessible points = 1.400000 m= 27965 mr = 49978 m= 5442 mr = 20346 m= 524 mr = 3453 m= 13 mr = 273 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 2381 time to turn everything in is 0.3800000 number of dielectric boundary points 34502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 95 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 16019 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) : 0.6819531 object centre at (A) : 13.89850 40.04800 24.26100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7251253E-02 -1.3568563E-02 midg,1,midg; midg,igrid,midg 3.1049760E-02 6.1817117E-02 1,midg,midg; igrid,midg,midg 6.8904273E-02 4.3060265E-02 gauss-seidel spectral radius is 0.9987781 estimated iterations to convergence 227 setup time was (sec) 0.6000000 now iterating at: 23:50:06 rms-change max change #iterations 4.269481 219.7099 at 10iterations 2.075068 87.03711 at 20iterations 1.007667 33.60501 at 30iterations 0.4895800 15.58786 at 40iterations 0.2383351 7.642607 at 50iterations 0.1155529 3.794900 at 60iterations 5.6540500E-02 1.821644 at 70iterations 2.7647151E-02 0.8814125 at 80iterations 1.3420303E-02 0.4042139 at 90iterations 6.5408987E-03 0.1988559 at 100iterations 3.1968185E-03 9.7554207E-02 at 110iterations 1.5596560E-03 5.0508499E-02 at 120iterations finished qdiffx linear iterations at : 23:50:14 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 1.5596560E-03 5.0508499E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 23:50:14 8.111u 0.223s 0:08.73 95.4% 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 Sat Oct 8 2011 at 23:50:14 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 = 2153 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.068789 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): -12.20300 40.00000 ymin,ymax (A): 14.17800 65.91800 zmin,zma (A): 3.129000 45.39300 x,y,z range (A): 52.20300 51.74000 42.26400 scale (grids/A): 3.068789 object centre (A): 13.89850 40.04800 24.26100 number of atom coordinates read : 2153 total number of charged atoms : 2018 net assigned charge : 9.500023 assigned positive charge : 310.3229 centred at (gu) : 85.41472 83.49808 83.16756 assigned negative charge : -300.8232 centred at (gu) : 85.68442 83.36248 83.62355 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 171944 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21077 grid for indexing accessible points = 1.400000 m= 87509 mr = 121293 m= 34991 mr = 70688 m= 10181 mr = 27893 m= 2027 mr = 7613 m= 249 mr = 1477 m= 10 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 7961 time to turn everything in is 0.9900000 number of dielectric boundary points 77807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 16144 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) : 2.045860 object centre at (A) : 13.89850 40.04800 24.26100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2906068 -0.1637073 midg,1,midg; midg,igrid,midg 0.3310600 0.7018288 1,midg,midg; igrid,midg,midg 0.5440348 0.3925588 gauss-seidel spectral radius is 0.9993073 estimated iterations to convergence 300 setup time was (sec) 1.240000 now iterating at: 23:50:16 rms-change max change #iterations 9.923699 395.8900 at 10iterations 5.927754 158.8904 at 20iterations 3.535732 71.42573 at 30iterations 2.104299 42.82143 at 40iterations 1.246537 24.94391 at 50iterations 0.7340544 14.54301 at 60iterations 0.4338460 9.244436 at 70iterations 0.2549495 4.941692 at 80iterations 0.1501255 2.747253 at 90iterations 8.7935388E-02 1.627506 at 100iterations 5.1655494E-02 1.137907 at 110iterations 3.0251265E-02 0.5509377 at 120iterations 1.7753443E-02 0.2994165 at 130iterations 1.0394955E-02 0.1837959 at 140iterations 6.0960026E-03 0.1225700 at 150iterations 3.5666104E-03 6.5614700E-02 at 160iterations 2.0933680E-03 3.8429260E-02 at 170iterations 1.2220944E-03 2.1026611E-02 at 180iterations finished qdiffx linear iterations at : 23:50:27 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 1.2220944E-03 2.1026611E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 23:50:28 13.055u 0.200s 0:13.65 97.0% 0+0k 0+0io 0pf+0w