Mon Oct 10 17:02:14 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 17:02:14 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4588 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5242310 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): -24.04300 40.06600 ymin,ymax (A): -18.05700 47.19500 zmin,zma (A): 7.120000 75.02900 x,y,z range (A): 64.10900 65.25200 67.90900 scale (grids/A): 0.5242310 object centre (A): 8.011501 14.56900 41.07450 number of atom coordinates read : 4588 total number of charged atoms : 4349 net assigned charge : 7.800026 assigned positive charge : 695.8467 centred at (gu) : 91.28497 88.49300 87.51746 assigned negative charge : -688.0505 centred at (gu) : 91.39057 88.60828 87.37208 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8054 nv = 96 ne = 84 npr = 91458 no. pairs analyzed = 91458 no. exposed pairs = 6062 no. arc points = 41694 no. surface atoms = 2024 nbur = 2564 mkacc time = 0.2000000 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 = 1.624000 m= 311 mr = 4037 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4043 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 10610 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4152790E-10 4.4356868E-10 midg,1,midg; midg,igrid,midg 1.0476111E-09 -1.9664244E-10 1,midg,midg; igrid,midg,midg 4.8025006E-10 -3.5607375E-10 gauss-seidel spectral radius is 0.9813780 estimated iterations to convergence 60 setup time was (sec) 0.6500000 now iterating at: 17:02:15 rms-change max change #iterations 7.4748635E-02 11.31328 at 10iterations 5.0318870E-03 0.7100220 at 20iterations 8.5441832E-04 0.1234398 at 30iterations 3.3102764E-04 5.5491447E-02 at 40iterations 1.4065825E-04 2.4562836E-02 at 50iterations finished qdiffx linear iterations at : 17:02:17 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.4065825E-04 2.4562836E-02 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 17:02:18 3.247u 0.163s 0:03.91 86.9% 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 17:02:18 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4588 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.572693 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): -24.04300 40.06600 ymin,ymax (A): -18.05700 47.19500 zmin,zma (A): 7.120000 75.02900 x,y,z range (A): 64.10900 65.25200 67.90900 scale (grids/A): 1.572693 object centre (A): 8.011501 14.56900 41.07450 number of atom coordinates read : 4588 total number of charged atoms : 4349 net assigned charge : 7.800026 assigned positive charge : 695.8467 centred at (gu) : 93.85303 85.47772 82.55101 assigned negative charge : -688.0505 centred at (gu) : 94.17135 85.82451 82.11580 start vw surface at 0.2400000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 90824 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41694 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 26912 mr = 61314 m= 2558 mr = 17774 m= 71 mr = 1054 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 40219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 489 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 32948 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) : 0.5242310 object centre at (A) : 8.011501 14.56900 41.07450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1362345E-03 2.4145905E-02 midg,1,midg; midg,igrid,midg 8.0738738E-03 -9.6013304E-03 1,midg,midg; igrid,midg,midg 1.4583142E-02 2.1622216E-03 gauss-seidel spectral radius is 0.9982039 estimated iterations to convergence 187 setup time was (sec) 0.9700000 now iterating at: 17:02:20 rms-change max change #iterations 3.970239 166.3132 at 10iterations 1.660670 66.11594 at 20iterations 0.6975135 25.57902 at 30iterations 0.2919167 9.877014 at 40iterations 0.1226474 4.176929 at 50iterations 5.1669739E-02 1.610825 at 60iterations 2.1724142E-02 0.6955471 at 70iterations 9.2846947E-03 0.3074299 at 80iterations 4.0574078E-03 0.1358819 at 90iterations 1.9003145E-03 6.1576843E-02 at 100iterations 9.9846686E-04 3.4963608E-02 at 110iterations 6.1136694E-04 2.1927834E-02 at 120iterations finished qdiffx linear iterations at : 17:02:26 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 6.1136694E-04 2.1927834E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 17:02:28 7.649u 0.284s 0:09.25 85.6% 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 17:02:28 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4588 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.359039 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): -24.04300 40.06600 ymin,ymax (A): -18.05700 47.19500 zmin,zma (A): 7.120000 75.02900 x,y,z range (A): 64.10900 65.25200 67.90900 scale (grids/A): 2.359039 object centre (A): 8.011501 14.56900 41.07450 number of atom coordinates read : 4588 total number of charged atoms : 4349 net assigned charge : 7.800026 assigned positive charge : 695.8467 centred at (gu) : 95.77935 83.21604 78.82618 assigned negative charge : -688.0505 centred at (gu) : 96.25695 83.73665 78.17361 start vw surface at 0.1800000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 211587 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41694 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 95949 mr = 151454 m= 25133 mr = 74260 m= 3744 mr = 17848 m= 214 mr = 2163 m= 3 mr = 80 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 90826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 34732 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) : 1.572693 object centre at (A) : 8.011501 14.56900 41.07450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4905910 0.4932904 midg,1,midg; midg,igrid,midg 8.8515453E-02 -0.2061980 1,midg,midg; igrid,midg,midg 0.2797920 6.0751978E-02 gauss-seidel spectral radius is 0.9991866 estimated iterations to convergence 277 setup time was (sec) 1.820000 now iterating at: 17:02:30 rms-change max change #iterations 10.51429 358.3699 at 10iterations 6.058832 144.9528 at 20iterations 3.468228 80.62718 at 30iterations 1.974480 40.24149 at 40iterations 1.122366 25.75973 at 50iterations 0.6342502 12.06116 at 60iterations 0.3580391 7.334541 at 70iterations 0.2020345 4.918558 at 80iterations 0.1136257 2.111620 at 90iterations 6.3939877E-02 1.287250 at 100iterations 3.5952143E-02 0.8286743 at 110iterations 2.0194134E-02 0.3970222 at 120iterations 1.1323929E-02 0.2457504 at 130iterations 6.3617150E-03 0.1281891 at 140iterations 3.5643703E-03 7.7103615E-02 at 150iterations 1.9957994E-03 3.4887791E-02 at 160iterations 1.1228662E-03 2.0948887E-02 at 170iterations 6.3046627E-04 1.3237000E-02 at 180iterations finished qdiffx linear iterations at : 17:02:40 total time elapsed so far: 12.10000 # loops : 180 mean,max change (kT/e) : 6.3046627E-04 1.3237000E-02 energy calculations done at 12.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 17:02:41 12.284u 0.291s 0:13.17 95.4% 0+0k 0+0io 0pf+0w