Sun Oct 9 13:11:12 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 Sun Oct 9 2011 at 13:11:12 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2343 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6967686 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): -6.013000 44.44900 ymin,ymax (A): -14.36400 36.72900 zmin,zma (A): 2.317000 44.56700 x,y,z range (A): 50.46200 51.09300 42.25000 scale (grids/A): 0.6967686 object centre (A): 19.21800 11.18250 23.44200 number of atom coordinates read : 2343 total number of charged atoms : 2203 net assigned charge : 4.500012 assigned positive charge : 359.3712 centred at (gu) : 89.32590 91.15157 90.84879 assigned negative charge : -354.8716 centred at (gu) : 89.33460 91.27544 90.90783 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7943 nv = 96 ne = 84 npr = 45762 no. pairs analyzed = 45762 no. exposed pairs = 3035 no. arc points = 20997 no. surface atoms = 1011 nbur = 1332 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 533 mr = 4486 m= 1 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1952 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8742 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7571561E-08 4.5570077E-09 midg,1,midg; midg,igrid,midg 6.7110385E-08 -3.2095901E-08 1,midg,midg; igrid,midg,midg 3.8862975E-08 2.3301240E-08 gauss-seidel spectral radius is 0.9892989 estimated iterations to convergence 79 setup time was (sec) 0.6400000 now iterating at: 13:11:13 rms-change max change #iterations 0.2048173 32.86531 at 10iterations 2.5116222E-02 3.229909 at 20iterations 3.7580037E-03 0.5256348 at 30iterations 9.3279203E-04 0.1605453 at 40iterations 3.1829093E-04 5.3169250E-02 at 50iterations finished qdiffx linear iterations at : 13:11:18 total time elapsed so far: 5.400000 # loops : 50 mean,max change (kT/e) : 3.1829093E-04 5.3169250E-02 energy calculations done at 5.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.570000 DelPhi exited at 13:11:18 5.571u 0.435s 0:06.27 95.6% 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 Sun Oct 9 2011 at 13:11:18 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2343 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.090306 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): -6.013000 44.44900 ymin,ymax (A): -14.36400 36.72900 zmin,zma (A): 2.317000 44.56700 x,y,z range (A): 50.46200 51.09300 42.25000 scale (grids/A): 2.090306 object centre (A): 19.21800 11.18250 23.44200 number of atom coordinates read : 2343 total number of charged atoms : 2203 net assigned charge : 4.500012 assigned positive charge : 359.3712 centred at (gu) : 87.97733 93.45406 92.54591 assigned negative charge : -354.8716 centred at (gu) : 88.00354 93.82628 92.72337 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20997 grid for indexing accessible points = 1.400000 m= 34458 mr = 59047 m= 6467 mr = 25894 m= 544 mr = 4227 m= 17 mr = 281 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 36224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 17477 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) : 0.6967686 object centre at (A) : 19.21800 11.18250 23.44200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0603479E-02 1.1920775E-02 midg,1,midg; midg,igrid,midg 1.8441239E-02 -3.4932081E-02 1,midg,midg; igrid,midg,midg 5.7294201E-02 -1.5128396E-02 gauss-seidel spectral radius is 0.9988366 estimated iterations to convergence 232 setup time was (sec) 1.080000 now iterating at: 13:11:25 rms-change max change #iterations 4.867625 215.2088 at 10iterations 2.397484 77.03848 at 20iterations 1.187937 34.26164 at 30iterations 0.5892230 18.59307 at 40iterations 0.2931859 8.892185 at 50iterations 0.1457529 4.242462 at 60iterations 7.2630033E-02 1.985834 at 70iterations 3.6333054E-02 1.094367 at 80iterations 1.8232301E-02 0.5722027 at 90iterations 9.2841368E-03 0.2913008 at 100iterations 4.8037576E-03 0.1489258 at 110iterations 2.5918353E-03 8.6116791E-02 at 120iterations finished qdiffx linear iterations at : 13:11:37 total time elapsed so far: 13.91000 # loops : 120 mean,max change (kT/e) : 2.5918353E-03 8.6116791E-02 energy calculations done at 13.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.08000 DelPhi exited at 13:11:38 14.080u 0.545s 0:19.49 75.0% 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 Sun Oct 9 2011 at 13:11:38 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2343 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.135459 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): -6.013000 44.44900 ymin,ymax (A): -14.36400 36.72900 zmin,zma (A): 2.317000 44.56700 x,y,z range (A): 50.46200 51.09300 42.25000 scale (grids/A): 3.135459 object centre (A): 19.21800 11.18250 23.44200 number of atom coordinates read : 2343 total number of charged atoms : 2203 net assigned charge : 4.500012 assigned positive charge : 359.3712 centred at (gu) : 86.96592 95.18107 93.81868 assigned negative charge : -354.8716 centred at (gu) : 87.00526 95.73934 94.08501 start vw surface at 0.1300000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 193688 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20997 grid for indexing accessible points = 1.400000 m= 106290 mr = 141701 m= 43669 mr = 88000 m= 12142 mr = 35775 m= 2309 mr = 9325 m= 303 mr = 1643 m= 24 mr = 218 m= 0 mr = 18 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.260000 number of dielectric boundary points 81745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.440000 number of grid points assigned charge 17624 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) : 2.090306 object centre at (A) : 19.21800 11.18250 23.44200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4758944 -1.5964705E-02 midg,1,midg; midg,igrid,midg 0.3077680 -0.5167320 1,midg,midg; igrid,midg,midg 0.5496107 -0.4495228 gauss-seidel spectral radius is 0.9993008 estimated iterations to convergence 298 setup time was (sec) 2.680000 now iterating at: 13:11:41 rms-change max change #iterations 11.01639 429.7966 at 10iterations 6.555681 131.1849 at 20iterations 3.897389 79.14394 at 30iterations 2.309391 42.18242 at 40iterations 1.367819 23.41652 at 50iterations 0.8056687 14.20920 at 60iterations 0.4750827 9.294323 at 70iterations 0.2794028 5.188784 at 80iterations 0.1642793 2.954847 at 90iterations 9.6596926E-02 1.601089 at 100iterations 5.6972086E-02 0.9888954 at 110iterations 3.3777658E-02 0.5830727 at 120iterations 2.0213889E-02 0.3756104 at 130iterations 1.2348007E-02 0.2201609 at 140iterations 7.8163091E-03 0.1549072 at 150iterations 5.1958216E-03 0.1084747 at 160iterations 3.6828984E-03 7.7957153E-02 at 170iterations 2.7725201E-03 5.8834076E-02 at 180iterations finished qdiffx linear iterations at : 13:12:02 total time elapsed so far: 23.75000 # loops : 180 mean,max change (kT/e) : 2.7725201E-03 5.8834076E-02 energy calculations done at 23.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.91000 DelPhi exited at 13:12:03 23.919u 0.531s 0:24.74 98.7% 0+0k 0+0io 0pf+0w