Wed Dec 28 11:04:07 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 11:04:07 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 0.6448341 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): -6.128000 35.09600 ymin,ymax (A): -3.976000 49.75300 zmin,zma (A): -24.32800 30.88000 x,y,z range (A): 41.22400 53.72900 55.20800 scale (grids/A): 0.6448341 object centre (A): 14.48400 22.88850 3.276001 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 290.6260 centred at (gu) : 90.82236 92.47556 90.22374 assigned negative charge : -286.6263 centred at (gu) : 90.91383 92.58645 90.16322 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5621 nv = 96 ne = 84 npr = 40206 no. pairs analyzed = 40206 no. exposed pairs = 2359 no. arc points = 16824 no. surface atoms = 807 nbur = 1155 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 282 mr = 3193 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 91 time to turn everything in is 0.3000000 number of dielectric boundary points 2662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1719 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 6610 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0508751E-09 1.3489886E-08 midg,1,midg; midg,igrid,midg 1.0537113E-08 -7.0922708E-09 1,midg,midg; igrid,midg,midg 1.3313791E-08 -2.4451112E-09 gauss-seidel spectral radius is 0.9874820 estimated iterations to convergence 73 setup time was (sec) 0.8000000 now iterating at: 11:04:08 rms-change max change #iterations 0.1289559 21.30937 at 10iterations 1.3174389E-02 1.918727 at 20iterations 1.3385835E-03 0.2568655 at 30iterations 1.3228679E-04 2.0267487E-02 at 40iterations 1.3278229E-05 1.9249916E-03 at 50iterations finished qdiffx linear iterations at : 11:04:15 total time elapsed so far: 7.040000 # loops : 50 mean,max change (kT/e) : 1.3278229E-05 1.9249916E-03 energy calculations done at 7.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.220000 DelPhi exited at 11:04:15 7.223u 0.680s 0:08.28 95.4% 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 11:04:15 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.934502 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): -6.128000 35.09600 ymin,ymax (A): -3.976000 49.75300 zmin,zma (A): -24.32800 30.88000 x,y,z range (A): 41.22400 53.72900 55.20800 scale (grids/A): 1.934502 object centre (A): 14.48400 22.88850 3.276001 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 290.6260 centred at (gu) : 92.46698 97.42657 90.67117 assigned negative charge : -286.6263 centred at (gu) : 92.74179 97.75943 90.48974 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16824 grid for indexing accessible points = 1.400000 m= 23094 mr = 42482 m= 3564 mr = 17997 m= 211 mr = 2328 m= 7 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 2898 time to turn everything in is 0.6400000 number of dielectric boundary points 24559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 14434 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) : 0.6448341 object centre at (A) : 14.48400 22.88850 3.276001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3172956E-02 2.0542646E-02 midg,1,midg; midg,igrid,midg 2.7781550E-02 -3.4815820E-03 1,midg,midg; igrid,midg,midg 1.0535343E-02 -1.8244832E-03 gauss-seidel spectral radius is 0.9985971 estimated iterations to convergence 212 setup time was (sec) 1.180000 now iterating at: 11:04:17 rms-change max change #iterations 3.715356 199.8202 at 10iterations 1.730063 63.80643 at 20iterations 0.8013346 30.60571 at 30iterations 0.3727313 13.86462 at 40iterations 0.1721581 6.354958 at 50iterations 7.9415418E-02 2.966245 at 60iterations 3.6977697E-02 1.453205 at 70iterations 1.7106293E-02 0.5922270 at 80iterations 7.9280483E-03 0.3386612 at 90iterations 3.6828113E-03 0.1313324 at 100iterations 1.7044209E-03 6.1128736E-02 at 110iterations 7.9134217E-04 2.5944710E-02 at 120iterations finished qdiffx linear iterations at : 11:04:34 total time elapsed so far: 17.73000 # loops : 120 mean,max change (kT/e) : 7.9134217E-04 2.5944710E-02 energy calculations done at 17.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.90000 DelPhi exited at 11:04:35 17.906u 0.760s 0:19.46 95.8% 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 Wed Dec 28 2011 at 11:04:35 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 2.901753 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): -6.128000 35.09600 ymin,ymax (A): -3.976000 49.75300 zmin,zma (A): -24.32800 30.88000 x,y,z range (A): 41.22400 53.72900 55.20800 scale (grids/A): 2.901753 object centre (A): 14.48400 22.88850 3.276001 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 290.6260 centred at (gu) : 93.70052 101.1398 91.00671 assigned negative charge : -286.6263 centred at (gu) : 94.11281 101.6392 90.73475 start vw surface at 0.1200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 140033 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16824 grid for indexing accessible points = 1.400000 m= 74179 mr = 102526 m= 27754 mr = 62469 m= 6351 mr = 23230 m= 886 mr = 4946 m= 58 mr = 583 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 10407 time to turn everything in is 1.600000 number of dielectric boundary points 55483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 14640 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) : 1.934502 object centre at (A) : 14.48400 22.88850 3.276001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.023467 6.1513260E-02 midg,1,midg; midg,igrid,midg 0.2463749 -7.2327107E-02 1,midg,midg; igrid,midg,midg 6.6284209E-02 -9.8097008E-03 gauss-seidel spectral radius is 0.9992346 estimated iterations to convergence 285 setup time was (sec) 2.200000 now iterating at: 11:04:38 rms-change max change #iterations 8.634390 387.4044 at 10iterations 4.935073 120.0574 at 20iterations 2.811991 70.77023 at 30iterations 1.599278 32.71621 at 40iterations 0.9079970 19.06745 at 50iterations 0.5169331 11.42085 at 60iterations 0.2925677 5.959537 at 70iterations 0.1663117 3.714293 at 80iterations 9.4528235E-02 1.931005 at 90iterations 5.3635590E-02 1.062138 at 100iterations 3.0458601E-02 0.6556383 at 110iterations 1.7272372E-02 0.3288991 at 120iterations 9.8154508E-03 0.1824708 at 130iterations 5.5730417E-03 0.1137733 at 140iterations 3.1624760E-03 5.9486389E-02 at 150iterations 1.8001971E-03 3.7458420E-02 at 160iterations 1.0191631E-03 2.1816254E-02 at 170iterations 5.8031274E-04 1.0437012E-02 at 180iterations finished qdiffx linear iterations at : 11:05:07 total time elapsed so far: 30.89000 # loops : 180 mean,max change (kT/e) : 5.8031274E-04 1.0437012E-02 energy calculations done at 30.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 31.07000 DelPhi exited at 11:05:07 31.072u 0.858s 0:32.45 98.3% 0+0k 0+0io 0pf+0w