Sat Oct 8 16:22:25 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 16:22:25 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 = 2367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5834344 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): -2.260000 46.88800 ymin,ymax (A): -15.88500 29.94000 zmin,zma (A): -19.16500 41.85300 x,y,z range (A): 49.14799 45.82500 61.01800 scale (grids/A): 0.5834344 object centre (A): 22.31400 7.027501 11.34400 number of atom coordinates read : 2367 total number of charged atoms : 2288 net assigned charge : 4.000001 assigned positive charge : 352.0741 centred at (gu) : 90.02431 88.84247 88.87532 assigned negative charge : -348.0747 centred at (gu) : 90.05746 88.96612 88.90449 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5231 nv = 96 ne = 84 npr = 48099 no. pairs analyzed = 48099 no. exposed pairs = 2953 no. arc points = 20579 no. surface atoms = 1001 nbur = 1366 mkacc time = 9.0000004E-02 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 = 1.484000 m= 215 mr = 2785 m= 0 mr = 15 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.1800000 number of dielectric boundary points 2646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2047 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6799 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9523809E-09 3.0281525E-10 midg,1,midg; midg,igrid,midg 4.3238164E-09 -1.1100646E-09 1,midg,midg; igrid,midg,midg 1.5730676E-09 3.0577421E-10 gauss-seidel spectral radius is 0.9847829 estimated iterations to convergence 67 setup time was (sec) 0.3600000 now iterating at: 16:22:25 rms-change max change #iterations 8.7311432E-02 16.26246 at 10iterations 7.0399428E-03 1.380533 at 20iterations 5.9265806E-04 9.3080521E-02 at 30iterations 6.9795256E-05 1.2930632E-02 at 40iterations 1.4090814E-05 3.1480789E-03 at 50iterations finished qdiffx linear iterations at : 16:22:28 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.4090814E-05 3.1480789E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 16:22:28 3.348u 0.168s 0:03.79 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 16:22:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.750303 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): -2.260000 46.88800 ymin,ymax (A): -15.88500 29.94000 zmin,zma (A): -19.16500 41.85300 x,y,z range (A): 49.14799 45.82500 61.01800 scale (grids/A): 1.750303 object centre (A): 22.31400 7.027501 11.34400 number of atom coordinates read : 2367 total number of charged atoms : 2288 net assigned charge : 4.000001 assigned positive charge : 352.0741 centred at (gu) : 90.07234 86.52697 86.62555 assigned negative charge : -348.0747 centred at (gu) : 90.17233 86.89816 86.71342 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 57848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20579 grid for indexing accessible points = 1.400000 m= 18427 mr = 39657 m= 2306 mr = 13091 m= 84 mr = 1381 m= 0 mr = 24 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 644 time to turn everything in is 0.2900000 number of dielectric boundary points 24512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 17821 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) : 0.5834344 object centre at (A) : 22.31400 7.027501 11.34400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9633964E-02 1.6282909E-02 midg,1,midg; midg,igrid,midg 1.2788296E-02 -1.6910092E-03 1,midg,midg; igrid,midg,midg 2.9390326E-03 -1.6560070E-02 gauss-seidel spectral radius is 0.9983588 estimated iterations to convergence 196 setup time was (sec) 0.5000000 now iterating at: 16:22:29 rms-change max change #iterations 3.329826 161.3770 at 10iterations 1.454820 61.62644 at 20iterations 0.6339517 26.60462 at 30iterations 0.2767607 10.56178 at 40iterations 0.1204771 4.335733 at 50iterations 5.2472655E-02 1.831628 at 60iterations 2.2844646E-02 0.8638473 at 70iterations 9.9958126E-03 0.3904390 at 80iterations 4.3523945E-03 0.1607704 at 90iterations 1.8952490E-03 6.7999125E-02 at 100iterations 8.3290262E-04 3.0737519E-02 at 110iterations 3.6499798E-04 1.3684750E-02 at 120iterations finished qdiffx linear iterations at : 16:22:36 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 3.6499798E-04 1.3684750E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 16:22:37 7.531u 0.193s 0:08.01 96.3% 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 16:22:37 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 = 2367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.625455 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): -2.260000 46.88800 ymin,ymax (A): -15.88500 29.94000 zmin,zma (A): -19.16500 41.85300 x,y,z range (A): 49.14799 45.82500 61.01800 scale (grids/A): 2.625455 object centre (A): 22.31400 7.027501 11.34400 number of atom coordinates read : 2367 total number of charged atoms : 2288 net assigned charge : 4.000001 assigned positive charge : 352.0741 centred at (gu) : 90.10835 84.79043 84.93824 assigned negative charge : -348.0747 centred at (gu) : 90.25849 85.34719 85.07009 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 134210 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20579 grid for indexing accessible points = 1.400000 m= 62383 mr = 96680 m= 19778 mr = 50041 m= 3999 mr = 15553 m= 364 mr = 2995 m= 12 mr = 223 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 2124 time to turn everything in is 0.7100000 number of dielectric boundary points 55254 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 18290 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) : 1.750303 object centre at (A) : 22.31400 7.027501 11.34400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2317603 0.4616754 midg,1,midg; midg,igrid,midg 0.1391111 -2.5032483E-02 1,midg,midg; igrid,midg,midg 4.3975245E-02 -0.2686266 gauss-seidel spectral radius is 0.9991755 estimated iterations to convergence 275 setup time was (sec) 0.9300000 now iterating at: 16:22:38 rms-change max change #iterations 8.252427 262.6927 at 10iterations 4.669414 114.7022 at 20iterations 2.634103 60.93655 at 30iterations 1.484501 32.56395 at 40iterations 0.8316206 19.75808 at 50iterations 0.4662291 11.59664 at 60iterations 0.2609760 6.188669 at 70iterations 0.1459671 3.342476 at 80iterations 8.1474379E-02 1.710175 at 90iterations 4.5490049E-02 0.9660215 at 100iterations 2.5442520E-02 0.5414834 at 110iterations 1.4179852E-02 0.3067331 at 120iterations 7.9182256E-03 0.1816301 at 130iterations 4.4167116E-03 0.1054811 at 140iterations 2.4648826E-03 5.7596207E-02 at 150iterations 1.3824429E-03 3.0775428E-02 at 160iterations 7.7451731E-04 1.6692638E-02 at 170iterations 4.3780878E-04 1.0146260E-02 at 180iterations finished qdiffx linear iterations at : 16:22:49 total time elapsed so far: 11.97000 # loops : 180 mean,max change (kT/e) : 4.3780878E-04 1.0146260E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.11000 DelPhi exited at 16:22:49 12.110u 0.204s 0:12.58 97.8% 0+0k 0+0io 0pf+0w