Sat Oct 8 16:38:10 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 Sat Oct 8 2011 at 16:38:10 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 = 4484 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5460292 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): 20.38900 79.55300 ymin,ymax (A): 118.2270 183.4250 zmin,zma (A): -1.051000 60.12000 x,y,z range (A): 59.16400 65.19798 61.17100 scale (grids/A): 0.5460292 object centre (A): 49.97100 150.8260 29.53450 number of atom coordinates read : 4484 total number of charged atoms : 4314 net assigned charge : 2.500044 assigned positive charge : 685.7846 centred at (gu) : 90.80603 89.64903 87.48154 assigned negative charge : -683.2880 centred at (gu) : 90.79407 89.58124 87.50892 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8625 nv = 96 ne = 84 npr = 90391 no. pairs analyzed = 90391 no. exposed pairs = 5595 no. arc points = 38554 no. surface atoms = 1873 nbur = 2611 mkacc time = 0.2300000 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 = 1.568000 m= 383 mr = 4577 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.4800000 number of dielectric boundary points 4403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4024 ## 537 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 11524 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0073764E-10 -6.7266186E-11 midg,1,midg; midg,igrid,midg -5.9624067E-10 7.6079232E-10 1,midg,midg; igrid,midg,midg 2.3215574E-11 3.2880693E-10 gauss-seidel spectral radius is 0.9828201 estimated iterations to convergence 63 setup time was (sec) 0.8000000 now iterating at: 16:38:11 rms-change max change #iterations 9.0018600E-02 11.50744 at 10iterations 6.7288508E-03 0.9610748 at 20iterations 1.1465816E-03 0.1602612 at 30iterations 3.8920974E-04 5.1969528E-02 at 40iterations 1.4284726E-04 1.8007278E-02 at 50iterations finished qdiffx linear iterations at : 16:38:15 total time elapsed so far: 4.630000 # loops : 50 mean,max change (kT/e) : 1.4284726E-04 1.8007278E-02 energy calculations done at 4.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.800000 DelPhi exited at 16:38:15 4.801u 0.386s 0:05.48 94.5% 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 Sat Oct 8 2011 at 16:38:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4484 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: 1.638088 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): 20.38900 79.55300 ymin,ymax (A): 118.2270 183.4250 zmin,zma (A): -1.051000 60.12000 x,y,z range (A): 59.16400 65.19798 61.17100 scale (grids/A): 1.638088 object centre (A): 49.97100 150.8260 29.53450 number of atom coordinates read : 4484 total number of charged atoms : 4314 net assigned charge : 2.500044 assigned positive charge : 685.7846 centred at (gu) : 92.41677 88.94608 82.44365 assigned negative charge : -683.2880 centred at (gu) : 92.38213 88.74325 82.52631 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 96859 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38554 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 30808 mr = 67642 m= 3495 mr = 21021 m= 102 mr = 1790 m= 0 mr = 8 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 409 time to turn everything in is 0.8000000 number of dielectric boundary points 40803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 439 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 33035 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) : 0.5460292 object centre at (A) : 49.97100 150.8260 29.53450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1964539E-03 8.4781274E-03 midg,1,midg; midg,igrid,midg 1.1393951E-02 3.2021236E-02 1,midg,midg; igrid,midg,midg -2.5314301E-02 -1.2571997E-02 gauss-seidel spectral radius is 0.9983473 estimated iterations to convergence 195 setup time was (sec) 1.100000 now iterating at: 16:38:17 rms-change max change #iterations 4.265055 152.0227 at 10iterations 1.844409 60.13699 at 20iterations 0.8006293 24.02629 at 30iterations 0.3476961 10.72201 at 40iterations 0.1511294 4.421341 at 50iterations 6.5847993E-02 2.011395 at 60iterations 2.8780553E-02 0.9215508 at 70iterations 1.2654203E-02 0.3722610 at 80iterations 5.6551369E-03 0.1633606 at 90iterations 2.6331039E-03 8.8538170E-02 at 100iterations 1.3151906E-03 4.0962219E-02 at 110iterations 7.2524854E-04 2.2617340E-02 at 120iterations finished qdiffx linear iterations at : 16:38:27 total time elapsed so far: 11.32000 # loops : 120 mean,max change (kT/e) : 7.2524854E-04 2.2617340E-02 energy calculations done at 11.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.49000 DelPhi exited at 16:38:28 11.496u 0.438s 0:12.18 97.8% 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 Sat Oct 8 2011 at 16:38:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4484 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: 2.457131 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): 20.38900 79.55300 ymin,ymax (A): 118.2270 183.4250 zmin,zma (A): -1.051000 60.12000 x,y,z range (A): 59.16400 65.19798 61.17100 scale (grids/A): 2.457131 object centre (A): 49.97100 150.8260 29.53450 number of atom coordinates read : 4484 total number of charged atoms : 4314 net assigned charge : 2.500044 assigned positive charge : 685.7846 centred at (gu) : 93.62505 88.41869 78.66532 assigned negative charge : -683.2880 centred at (gu) : 93.57313 88.11487 78.78966 start vw surface at 0.1600000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 224996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38554 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106171 mr = 165293 m= 31340 mr = 83916 m= 5661 mr = 23338 m= 450 mr = 3785 m= 15 mr = 222 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 1414 time to turn everything in is 1.980000 number of dielectric boundary points 92079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 34471 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) : 1.638088 object centre at (A) : 49.97100 150.8260 29.53450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7743282E-03 0.1877227 midg,1,midg; midg,igrid,midg 0.2082740 0.5674185 1,midg,midg; igrid,midg,midg -0.5055271 -0.1901993 gauss-seidel spectral radius is 0.9992213 estimated iterations to convergence 283 setup time was (sec) 2.340000 now iterating at: 16:38:30 rms-change max change #iterations 11.00821 298.0504 at 10iterations 6.392431 124.5972 at 20iterations 3.688322 81.65402 at 30iterations 2.123616 40.45970 at 40iterations 1.219229 20.97718 at 50iterations 0.6964519 11.94632 at 60iterations 0.3972810 8.610319 at 70iterations 0.2266894 3.946567 at 80iterations 0.1291445 2.541092 at 90iterations 7.3478982E-02 1.330111 at 100iterations 4.1689981E-02 0.7526836 at 110iterations 2.3766167E-02 0.4223862 at 120iterations 1.3499659E-02 0.2529945 at 130iterations 7.7021397E-03 0.1379648 at 140iterations 4.4075130E-03 7.9753876E-02 at 150iterations 2.5472066E-03 4.6895981E-02 at 160iterations 1.4932727E-03 2.7297974E-02 at 170iterations 8.9681800E-04 1.6496658E-02 at 180iterations finished qdiffx linear iterations at : 16:38:48 total time elapsed so far: 19.66000 # loops : 180 mean,max change (kT/e) : 8.9681800E-04 1.6496658E-02 energy calculations done at 19.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.83000 DelPhi exited at 16:38:48 19.833u 0.453s 0:20.56 98.6% 0+0k 0+0io 0pf+0w