Mon Oct 10 14:10:23 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 Mon Oct 10 2011 at 14:10:23 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: SEP 334 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5413461 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): -2.388000 50.42000 ymin,ymax (A): -11.08600 40.23100 zmin,zma (A): -17.61700 48.14500 x,y,z range (A): 52.80800 51.31700 65.76199 scale (grids/A): 0.5413461 object centre (A): 24.01600 14.57250 15.26400 number of atom coordinates read : 2701 total number of charged atoms : 2554 net assigned charge : 3.970007 assigned positive charge : 411.8646 centred at (gu) : 90.34737 90.98685 89.19255 assigned negative charge : -407.8954 centred at (gu) : 90.24367 90.85476 89.29788 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5229 nv = 96 ne = 84 npr = 52948 no. pairs analyzed = 52948 no. exposed pairs = 3542 no. arc points = 25240 no. surface atoms = 1190 nbur = 1511 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 = 1.596000 m= 223 mr = 2570 m= 0 mr = 17 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3400000 number of dielectric boundary points 2865 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2574 ## 361 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 6742 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8699914E-10 -2.8699051E-10 midg,1,midg; midg,igrid,midg -3.8395762E-10 1.0990678E-09 1,midg,midg; igrid,midg,midg -3.1550185E-10 7.8098994E-10 gauss-seidel spectral radius is 0.9823927 estimated iterations to convergence 62 setup time was (sec) 0.6000000 now iterating at: 14:10:24 rms-change max change #iterations 7.1177036E-02 12.72308 at 10iterations 5.0527835E-03 0.9004402 at 20iterations 5.8913720E-04 0.1039886 at 30iterations 1.2557546E-04 2.1854401E-02 at 40iterations 3.2175329E-05 5.5980682E-03 at 50iterations finished qdiffx linear iterations at : 14:10:27 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 3.2175329E-05 5.5980682E-03 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 14:10:28 3.992u 0.256s 0:04.83 87.7% 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 Mon Oct 10 2011 at 14:10:28 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: SEP 334 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.624038 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): -2.388000 50.42000 ymin,ymax (A): -11.08600 40.23100 zmin,zma (A): -17.61700 48.14500 x,y,z range (A): 52.80800 51.31700 65.76199 scale (grids/A): 1.624038 object centre (A): 24.01600 14.57250 15.26400 number of atom coordinates read : 2701 total number of charged atoms : 2554 net assigned charge : 3.970007 assigned positive charge : 411.8646 centred at (gu) : 91.04169 92.96007 87.57690 assigned negative charge : -407.8954 centred at (gu) : 90.73087 92.56409 87.89332 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 57770 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25240 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17740 mr = 38402 m= 1811 mr = 11778 m= 38 mr = 782 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 234 time to turn everything in is 0.5400000 number of dielectric boundary points 26397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 323 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19568 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) : 0.5413461 object centre at (A) : 24.01600 14.57250 15.26400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5424102E-02 4.1095996E-03 midg,1,midg; midg,igrid,midg 1.0611161E-05 1.0069972E-02 1,midg,midg; igrid,midg,midg -1.7772509E-02 1.8651506E-03 gauss-seidel spectral radius is 0.9981451 estimated iterations to convergence 184 setup time was (sec) 0.8200000 now iterating at: 14:10:29 rms-change max change #iterations 3.144773 146.7377 at 10iterations 1.299042 55.39309 at 20iterations 0.5337192 22.31878 at 30iterations 0.2196739 8.314960 at 40iterations 9.0427279E-02 3.602882 at 50iterations 3.7547711E-02 1.363627 at 60iterations 1.5539402E-02 0.6334548 at 70iterations 6.4410735E-03 0.2481337 at 80iterations 2.6889704E-03 0.1058636 at 90iterations 1.1367676E-03 4.3087006E-02 at 100iterations 4.9434311E-04 2.0854950E-02 at 110iterations 2.2390757E-04 9.4528198E-03 at 120iterations finished qdiffx linear iterations at : 14:10:37 total time elapsed so far: 8.820000 # loops : 120 mean,max change (kT/e) : 2.2390757E-04 9.4528198E-03 energy calculations done at 8.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.000000 DelPhi exited at 14:10:38 9.004u 0.263s 0:09.85 94.0% 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 Mon Oct 10 2011 at 14:10:38 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: SEP 334 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.436058 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): -2.388000 50.42000 ymin,ymax (A): -11.08600 40.23100 zmin,zma (A): -17.61700 48.14500 x,y,z range (A): 52.80800 51.31700 65.76199 scale (grids/A): 2.436058 object centre (A): 24.01600 14.57250 15.26400 number of atom coordinates read : 2701 total number of charged atoms : 2554 net assigned charge : 3.970007 assigned positive charge : 411.8646 centred at (gu) : 91.56241 94.44009 86.36526 assigned negative charge : -407.8954 centred at (gu) : 91.09617 93.84615 86.83995 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 134091 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25240 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 61286 mr = 94188 m= 17077 mr = 47518 m= 2726 mr = 12399 m= 198 mr = 1654 m= 6 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 945 time to turn everything in is 1.250000 number of dielectric boundary points 59528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 20404 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) : 1.624038 object centre at (A) : 24.01600 14.57250 15.26400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6785973 0.1280718 midg,1,midg; midg,igrid,midg 1.9519228E-02 0.1125693 1,midg,midg; igrid,midg,midg -0.3132305 1.6666323E-02 gauss-seidel spectral radius is 0.9991191 estimated iterations to convergence 266 setup time was (sec) 1.570000 now iterating at: 14:10:40 rms-change max change #iterations 8.243133 346.9542 at 10iterations 4.636263 134.8795 at 20iterations 2.592793 66.87080 at 30iterations 1.437398 34.89677 at 40iterations 0.7951428 19.71814 at 50iterations 0.4384415 11.70680 at 60iterations 0.2413224 5.598820 at 70iterations 0.1326199 3.078814 at 80iterations 7.2701827E-02 1.954933 at 90iterations 3.9933894E-02 0.8476105 at 100iterations 2.1883572E-02 0.4653215 at 110iterations 1.1994996E-02 0.2836170 at 120iterations 6.5694777E-03 0.1460867 at 130iterations 3.6039979E-03 7.8450203E-02 at 140iterations 1.9803655E-03 4.5771986E-02 at 150iterations 1.0931352E-03 2.3262024E-02 at 160iterations 6.0690386E-04 1.3240814E-02 at 170iterations 3.3968332E-04 7.2488785E-03 at 180iterations finished qdiffx linear iterations at : 14:10:53 total time elapsed so far: 14.52000 # loops : 180 mean,max change (kT/e) : 3.3968332E-04 7.2488785E-03 energy calculations done at 14.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.70000 DelPhi exited at 14:10:54 14.700u 0.295s 0:15.80 94.8% 0+0k 0+0io 0pf+0w