Mon Oct 10 10:08:15 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 10:08:15 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2696 !!! WARNING: HIT 228 has a net charge of 0.5140 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: 0.5768825 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): -18.40900 33.90000 ymin,ymax (A): -59.72300 -2.874000 zmin,zma (A): -1.520000 60.19100 x,y,z range (A): 52.30900 56.84900 61.71100 scale (grids/A): 0.5768825 object centre (A): 7.745499 -31.29850 29.33550 number of atom coordinates read : 2696 total number of charged atoms : 2547 net assigned charge : 5.014009 assigned positive charge : 394.6741 centred at (gu) : 88.61488 88.37197 87.71444 assigned negative charge : -389.6605 centred at (gu) : 88.72551 88.21130 87.73580 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6176 nv = 96 ne = 84 npr = 51377 no. pairs analyzed = 51377 no. exposed pairs = 4154 no. arc points = 30623 no. surface atoms = 1379 nbur = 1317 mkacc time = 0.1200000 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= 326 mr = 2704 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2939 ## 329 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7683 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3098654E-09 3.7533890E-10 midg,1,midg; midg,igrid,midg -2.7398532E-09 2.5240252E-09 1,midg,midg; igrid,midg,midg 3.9760928E-09 -6.6486178E-10 gauss-seidel spectral radius is 0.9844908 estimated iterations to convergence 66 setup time was (sec) 0.5800000 now iterating at: 10:08:16 rms-change max change #iterations 9.0584017E-02 15.73795 at 10iterations 6.8808650E-03 1.072792 at 20iterations 5.2733836E-04 8.6536169E-02 at 30iterations 4.0446557E-05 6.3848495E-03 at 40iterations 3.7315799E-06 5.3215027E-04 at 50iterations finished qdiffx linear iterations at : 10:08:18 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 3.7315799E-06 5.3215027E-04 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 10:08:19 3.592u 0.205s 0:04.08 92.8% 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 10:08:19 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2696 !!! WARNING: HIT 228 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.730648 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): -18.40900 33.90000 ymin,ymax (A): -59.72300 -2.874000 zmin,zma (A): -1.520000 60.19100 x,y,z range (A): 52.30900 56.84900 61.71100 scale (grids/A): 1.730648 object centre (A): 7.745499 -31.29850 29.33550 number of atom coordinates read : 2696 total number of charged atoms : 2547 net assigned charge : 5.014009 assigned positive charge : 394.6741 centred at (gu) : 85.84408 85.11538 83.14283 assigned negative charge : -389.6605 centred at (gu) : 86.17621 84.63376 83.20721 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 65883 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30623 grid for indexing accessible points = 1.400000 m= 21207 mr = 39914 m= 2765 mr = 13552 m= 108 mr = 1308 m= 0 mr = 10 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 35179 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19794 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) : 0.5768825 object centre at (A) : 7.745499 -31.29850 29.33550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0194344E-02 1.2842318E-03 midg,1,midg; midg,igrid,midg 1.7195303E-02 2.8419625E-02 1,midg,midg; igrid,midg,midg 1.2032871E-02 -8.7429589E-04 gauss-seidel spectral radius is 0.9983878 estimated iterations to convergence 198 setup time was (sec) 0.8500000 now iterating at: 10:08:20 rms-change max change #iterations 3.529014 164.7373 at 10iterations 1.538828 62.75913 at 20iterations 0.6749301 25.47803 at 30iterations 0.2961515 11.32336 at 40iterations 0.1296234 6.228036 at 50iterations 5.6804173E-02 2.001369 at 60iterations 2.4860565E-02 0.9533577 at 70iterations 1.0868774E-02 0.4113007 at 80iterations 4.7601545E-03 0.1819353 at 90iterations 2.0848049E-03 8.1729889E-02 at 100iterations 9.1416040E-04 3.2760620E-02 at 110iterations 4.0266436E-04 1.5071869E-02 at 120iterations finished qdiffx linear iterations at : 10:08:28 total time elapsed so far: 8.580000 # loops : 120 mean,max change (kT/e) : 4.0266436E-04 1.5071869E-02 energy calculations done at 8.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.780000 DelPhi exited at 10:08:28 8.780u 0.227s 0:09.38 95.9% 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 10:08:28 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2696 !!! WARNING: HIT 228 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.595971 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): -18.40900 33.90000 ymin,ymax (A): -59.72300 -2.874000 zmin,zma (A): -1.520000 60.19100 x,y,z range (A): 52.30900 56.84900 61.71100 scale (grids/A): 2.595971 object centre (A): 7.745499 -31.29850 29.33550 number of atom coordinates read : 2696 total number of charged atoms : 2547 net assigned charge : 5.014009 assigned positive charge : 394.6741 centred at (gu) : 83.76607 82.67300 79.71419 assigned negative charge : -389.6605 centred at (gu) : 84.26423 81.95058 79.81074 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 152392 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30623 grid for indexing accessible points = 1.400000 m= 69064 mr = 98782 m= 22711 mr = 51520 m= 4458 mr = 16438 m= 392 mr = 2788 m= 8 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 79317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 20367 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) : 1.730648 object centre at (A) : 7.745499 -31.29850 29.33550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4809258 3.1378027E-02 midg,1,midg; midg,igrid,midg 0.3626173 0.3467853 1,midg,midg; igrid,midg,midg 4.5396753E-02 -1.5280420E-02 gauss-seidel spectral radius is 0.9992175 estimated iterations to convergence 282 setup time was (sec) 1.620000 now iterating at: 10:08:30 rms-change max change #iterations 9.036587 333.5943 at 10iterations 5.312587 142.8625 at 20iterations 3.078952 81.76274 at 30iterations 1.775679 42.84066 at 40iterations 1.016378 26.91315 at 50iterations 0.5815862 14.39151 at 60iterations 0.3325292 8.727709 at 70iterations 0.1890427 4.543499 at 80iterations 0.1075488 2.297346 at 90iterations 6.1012857E-02 1.531425 at 100iterations 3.4646790E-02 0.7124119 at 110iterations 1.9573696E-02 0.4613228 at 120iterations 1.1099189E-02 0.2401528 at 130iterations 6.2749535E-03 0.1371994 at 140iterations 3.5497805E-03 8.0162048E-02 at 150iterations 2.0093534E-03 4.5505524E-02 at 160iterations 1.1362784E-03 2.6819229E-02 at 170iterations 6.4128306E-04 1.2977600E-02 at 180iterations finished qdiffx linear iterations at : 10:08:41 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 6.4128306E-04 1.2977600E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 10:08:42 13.110u 0.243s 0:13.63 97.9% 0+0k 0+0io 0pf+0w