Tue Oct 11 08:20:57 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 08:20:57 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 = 2745 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5690082 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): -28.79400 24.19300 ymin,ymax (A): -18.32100 36.80000 zmin,zma (A): -18.54700 44.01800 x,y,z range (A): 52.98700 55.12100 62.56500 scale (grids/A): 0.5690082 object centre (A): -2.300501 9.239499 12.73550 number of atom coordinates read : 2745 total number of charged atoms : 2598 net assigned charge : 8.000023 assigned positive charge : 419.7137 centred at (gu) : 92.12295 90.38175 91.71370 assigned negative charge : -411.7147 centred at (gu) : 92.21838 90.35763 91.64441 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5722 nv = 96 ne = 84 npr = 55211 no. pairs analyzed = 55211 no. exposed pairs = 3519 no. arc points = 25370 no. surface atoms = 1171 nbur = 1574 mkacc time = 0.1600000 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 = 1.512000 m= 235 mr = 2878 m= 0 mr = 12 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3800000 number of dielectric boundary points 3067 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2542 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7386 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5654622E-10 3.2255194E-09 midg,1,midg; midg,igrid,midg 7.7886231E-10 1.6632445E-09 1,midg,midg; igrid,midg,midg 1.5215598E-09 -3.1842820E-10 gauss-seidel spectral radius is 0.9840435 estimated iterations to convergence 65 setup time was (sec) 0.6600000 now iterating at: 08:20:58 rms-change max change #iterations 8.5117310E-02 15.74863 at 10iterations 6.3318545E-03 1.030420 at 20iterations 4.9167615E-04 7.3677063E-02 at 30iterations 4.8814156E-05 9.2296600E-03 at 40iterations 8.0481796E-06 1.2273788E-03 at 50iterations finished qdiffx linear iterations at : 08:21:01 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 8.0481796E-06 1.2273788E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 08:21:02 4.233u 0.192s 0:04.91 90.0% 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 08:21:02 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 = 2745 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.707025 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): -28.79400 24.19300 ymin,ymax (A): -18.32100 36.80000 zmin,zma (A): -18.54700 44.01800 x,y,z range (A): 52.98700 55.12100 62.56500 scale (grids/A): 1.707025 object centre (A): -2.300501 9.239499 12.73550 number of atom coordinates read : 2745 total number of charged atoms : 2598 net assigned charge : 8.000023 assigned positive charge : 419.7137 centred at (gu) : 96.36834 91.14474 95.14058 assigned negative charge : -411.7147 centred at (gu) : 96.65509 91.07267 94.93327 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 62183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25370 grid for indexing accessible points = 1.400000 m= 19757 mr = 41230 m= 2318 mr = 13502 m= 76 mr = 1217 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 548 time to turn everything in is 0.5800000 number of dielectric boundary points 28384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 20066 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) : 0.5690082 object centre at (A) : -2.300501 9.239499 12.73550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8802440E-03 1.8286031E-02 midg,1,midg; midg,igrid,midg -2.6642904E-03 7.5539732E-03 1,midg,midg; igrid,midg,midg 4.4912742E-03 5.5032163E-03 gauss-seidel spectral radius is 0.9983162 estimated iterations to convergence 193 setup time was (sec) 0.9300000 now iterating at: 08:21:03 rms-change max change #iterations 3.485460 224.2457 at 10iterations 1.498397 78.32246 at 20iterations 0.6474975 24.15888 at 30iterations 0.2776521 10.97874 at 40iterations 0.1195306 4.975780 at 50iterations 5.1485255E-02 1.876703 at 60iterations 2.2279976E-02 0.8577728 at 70iterations 9.5585696E-03 0.3926849 at 80iterations 4.1327286E-03 0.1479015 at 90iterations 1.7900622E-03 6.8874359E-02 at 100iterations 7.7184365E-04 2.9724121E-02 at 110iterations 3.3681007E-04 1.2760162E-02 at 120iterations finished qdiffx linear iterations at : 08:21:11 total time elapsed so far: 8.820000 # loops : 120 mean,max change (kT/e) : 3.3681007E-04 1.2760162E-02 energy calculations done at 8.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.040000 DelPhi exited at 08:21:12 9.047u 0.274s 0:09.87 94.3% 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 08:21:12 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 = 2745 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.560537 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): -28.79400 24.19300 ymin,ymax (A): -18.32100 36.80000 zmin,zma (A): -18.54700 44.01800 x,y,z range (A): 52.98700 55.12100 62.56500 scale (grids/A): 2.560537 object centre (A): -2.300501 9.239499 12.73550 number of atom coordinates read : 2745 total number of charged atoms : 2598 net assigned charge : 8.000023 assigned positive charge : 419.7137 centred at (gu) : 99.55222 91.71698 97.71068 assigned negative charge : -411.7147 centred at (gu) : 99.98244 91.60892 97.39986 start vw surface at 0.2000000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 144539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25370 grid for indexing accessible points = 1.400000 m= 66762 mr = 101222 m= 20219 mr = 52469 m= 3707 mr = 15099 m= 306 mr = 2516 m= 6 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 1773 time to turn everything in is 1.420000 number of dielectric boundary points 64090 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 20770 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) : 1.707025 object centre at (A) : -2.300501 9.239499 12.73550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4731815E-02 0.1815919 midg,1,midg; midg,igrid,midg -5.9389278E-02 -2.7914900E-02 1,midg,midg; igrid,midg,midg 1.4494720E-02 8.6478129E-02 gauss-seidel spectral radius is 0.9991749 estimated iterations to convergence 275 setup time was (sec) 1.820000 now iterating at: 08:21:14 rms-change max change #iterations 8.756699 306.2710 at 10iterations 4.950981 128.9589 at 20iterations 2.782043 63.90576 at 30iterations 1.562566 39.24449 at 40iterations 0.8742238 19.99891 at 50iterations 0.4886128 10.54842 at 60iterations 0.2736914 6.971184 at 70iterations 0.1529329 3.325138 at 80iterations 8.5356049E-02 1.891325 at 90iterations 4.7557790E-02 1.018147 at 100iterations 2.6535276E-02 0.5682659 at 110iterations 1.4763178E-02 0.3080654 at 120iterations 8.2406821E-03 0.1741943 at 130iterations 4.5768325E-03 9.5237732E-02 at 140iterations 2.5560306E-03 5.4391861E-02 at 150iterations 1.4247671E-03 3.5629272E-02 at 160iterations 7.9618773E-04 1.7515182E-02 at 170iterations 4.4588663E-04 8.9178085E-03 at 180iterations finished qdiffx linear iterations at : 08:21:27 total time elapsed so far: 14.34000 # loops : 180 mean,max change (kT/e) : 4.4588663E-04 8.9178085E-03 energy calculations done at 14.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.59000 DelPhi exited at 08:21:27 14.592u 0.184s 0:15.33 96.3% 0+0k 0+0io 0pf+0w