Wed Dec 28 11:01:48 PST 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 Wed Dec 28 2011 at 11:01:48 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6171020 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): -35.45700 10.13300 ymin,ymax (A): 1.710000 42.37400 zmin,zma (A): -27.72100 29.96800 x,y,z range (A): 45.59000 40.66400 57.68900 scale (grids/A): 0.6171020 object centre (A): -12.66200 22.04200 1.123501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 290.5720 centred at (gu) : 90.43073 89.19588 89.98730 assigned negative charge : -288.5722 centred at (gu) : 90.32674 89.37166 89.98828 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5225 nv = 96 ne = 84 npr = 39358 no. pairs analyzed = 39358 no. exposed pairs = 2471 no. arc points = 17131 no. surface atoms = 842 nbur = 1122 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 303 mr = 2959 m= 5 mr = 46 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 0.3100000 number of dielectric boundary points 2528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1774 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6215 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4364580E-09 1.3395939E-09 midg,1,midg; midg,igrid,midg 1.1041490E-08 -5.6289720E-09 1,midg,midg; igrid,midg,midg -3.0714287E-09 6.6679635E-09 gauss-seidel spectral radius is 0.9863510 estimated iterations to convergence 70 setup time was (sec) 0.6200000 now iterating at: 11:01:49 rms-change max change #iterations 0.1083628 19.22766 at 10iterations 9.8050656E-03 1.641312 at 20iterations 8.7765127E-04 0.1341276 at 30iterations 8.1663755E-05 1.4992714E-02 at 40iterations 7.4415584E-06 1.2028217E-03 at 50iterations finished qdiffx linear iterations at : 11:01:53 total time elapsed so far: 5.030000 # loops : 50 mean,max change (kT/e) : 7.4415584E-06 1.2028217E-03 energy calculations done at 5.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.230000 DelPhi exited at 11:01:55 5.231u 0.417s 0:06.69 84.3% 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 Wed Dec 28 2011 at 11:01:55 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.851306 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): -35.45700 10.13300 ymin,ymax (A): 1.710000 42.37400 zmin,zma (A): -27.72100 29.96800 x,y,z range (A): 45.59000 40.66400 57.68900 scale (grids/A): 1.851306 object centre (A): -12.66200 22.04200 1.123501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 290.5720 centred at (gu) : 91.29207 87.58768 89.96188 assigned negative charge : -288.5722 centred at (gu) : 90.98032 88.11512 89.96503 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 55834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17131 grid for indexing accessible points = 1.400000 m= 22386 mr = 38699 m= 3858 mr = 17541 m= 175 mr = 2560 m= 0 mr = 52 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 23401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 14370 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) : 0.6171020 object centre at (A) : -12.66200 22.04200 1.123501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9518038E-02 1.8902279E-02 midg,1,midg; midg,igrid,midg 2.1675478E-03 -1.2287000E-02 1,midg,midg; igrid,midg,midg -6.6006337E-03 -2.3052851E-03 gauss-seidel spectral radius is 0.9984838 estimated iterations to convergence 204 setup time was (sec) 0.8700000 now iterating at: 11:01:56 rms-change max change #iterations 3.428937 177.7434 at 10iterations 1.539604 65.90691 at 20iterations 0.6929204 29.15555 at 30iterations 0.3119855 11.63001 at 40iterations 0.1396054 5.579212 at 50iterations 6.2437154E-02 2.303478 at 60iterations 2.8189253E-02 1.105478 at 70iterations 1.2721794E-02 0.4667211 at 80iterations 5.7032076E-03 0.2075148 at 90iterations 2.5667150E-03 9.9758148E-02 at 100iterations 1.1581935E-03 4.3609619E-02 at 110iterations 5.1972416E-04 1.8066406E-02 at 120iterations finished qdiffx linear iterations at : 11:02:05 total time elapsed so far: 10.37000 # loops : 120 mean,max change (kT/e) : 5.1972416E-04 1.8066406E-02 energy calculations done at 10.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.56000 DelPhi exited at 11:02:08 10.561u 0.418s 0:13.80 79.4% 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 Wed Dec 28 2011 at 11:02:10 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.776959 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): -35.45700 10.13300 ymin,ymax (A): 1.710000 42.37400 zmin,zma (A): -27.72100 29.96800 x,y,z range (A): 45.59000 40.66400 57.68900 scale (grids/A): 2.776959 object centre (A): -12.66200 22.04200 1.123501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 290.5720 centred at (gu) : 91.93822 86.38160 89.94276 assigned negative charge : -288.5722 centred at (gu) : 91.47056 87.17274 89.94763 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 128683 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17131 grid for indexing accessible points = 1.400000 m= 69968 mr = 93311 m= 28558 mr = 58781 m= 7113 mr = 24288 m= 849 mr = 5571 m= 45 mr = 562 m= 0 mr = 29 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.410000 number of dielectric boundary points 52674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 14651 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) : 1.851306 object centre at (A) : -12.66200 22.04200 1.123501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5922200E-02 1.2003131E-02 midg,1,midg; midg,igrid,midg -3.2570779E-02 -0.1412552 1,midg,midg; igrid,midg,midg -9.2807718E-02 -7.2353765E-02 gauss-seidel spectral radius is 0.9991980 estimated iterations to convergence 279 setup time was (sec) 1.810000 now iterating at: 11:02:12 rms-change max change #iterations 8.190683 278.3435 at 10iterations 4.658847 143.9265 at 20iterations 2.627290 64.61394 at 30iterations 1.480809 31.42562 at 40iterations 0.8330653 18.47061 at 50iterations 0.4666637 10.97276 at 60iterations 0.2620925 5.613417 at 70iterations 0.1471804 2.927505 at 80iterations 8.2450017E-02 1.717067 at 90iterations 4.6301484E-02 1.036289 at 100iterations 2.6000526E-02 0.5863972 at 110iterations 1.4588151E-02 0.3064046 at 120iterations 8.1461007E-03 0.1655319 at 130iterations 4.5810267E-03 9.8304749E-02 at 140iterations 2.5612868E-03 5.1375389E-02 at 150iterations 1.4392111E-03 2.9163361E-02 at 160iterations 8.0679054E-04 1.6816139E-02 at 170iterations 4.5212993E-04 9.0751648E-03 at 180iterations finished qdiffx linear iterations at : 11:02:29 total time elapsed so far: 18.46000 # loops : 180 mean,max change (kT/e) : 4.5212993E-04 9.0751648E-03 energy calculations done at 18.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.66000 DelPhi exited at 11:02:31 18.661u 0.516s 0:21.21 90.3% 0+0k 0+0io 0pf+0w