Mon Oct 10 09:12:45 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 09:12:45 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 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: 0.6624612 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): -6.583000 35.04800 ymin,ymax (A): -4.261000 48.62000 zmin,zma (A): -23.64900 30.09000 x,y,z range (A): 41.63100 52.88100 53.73900 scale (grids/A): 0.6624612 object centre (A): 14.23250 22.17950 3.220500 number of atom coordinates read : 2004 total number of charged atoms : 1871 net assigned charge : 1.000005 assigned positive charge : 296.8839 centred at (gu) : 91.03823 92.98405 90.25616 assigned negative charge : -295.8843 centred at (gu) : 91.15116 93.05731 90.19512 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6027 nv = 96 ne = 84 npr = 41490 no. pairs analyzed = 41490 no. exposed pairs = 2385 no. arc points = 16986 no. surface atoms = 810 nbur = 1194 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 3464 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 130 time to turn everything in is 0.1700000 number of dielectric boundary points 2860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1658 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6904 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1250129E-09 1.3613707E-08 midg,1,midg; midg,igrid,midg 8.0204154E-09 -1.6254136E-08 1,midg,midg; igrid,midg,midg 1.6900355E-08 -1.8584306E-08 gauss-seidel spectral radius is 0.9881349 estimated iterations to convergence 75 setup time was (sec) 0.3600000 now iterating at: 09:12:46 rms-change max change #iterations 0.1507130 26.82761 at 10iterations 1.6268414E-02 2.807922 at 20iterations 1.7592165E-03 0.2508640 at 30iterations 1.8737860E-04 2.6950836E-02 at 40iterations 1.9510930E-05 2.8920174E-03 at 50iterations finished qdiffx linear iterations at : 09:12:49 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.9510930E-05 2.8920174E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 09:12:49 3.381u 0.176s 0:03.82 92.9% 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 09:12:49 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 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: 1.987383 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): -6.583000 35.04800 ymin,ymax (A): -4.261000 48.62000 zmin,zma (A): -23.64900 30.09000 x,y,z range (A): 41.63100 52.88100 53.73900 scale (grids/A): 1.987383 object centre (A): 14.23250 22.17950 3.220500 number of atom coordinates read : 2004 total number of charged atoms : 1871 net assigned charge : 1.000005 assigned positive charge : 296.8839 centred at (gu) : 93.11463 98.95202 90.76862 assigned negative charge : -295.8843 centred at (gu) : 93.45369 99.17205 90.58551 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63861 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16986 grid for indexing accessible points = 1.400000 m= 25058 mr = 44468 m= 4796 mr = 19627 m= 384 mr = 3404 m= 11 mr = 217 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2979 time to turn everything in is 0.3300000 number of dielectric boundary points 26395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14777 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) : 0.6624612 object centre at (A) : 14.23250 22.17950 3.220500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6365993E-02 9.3281325E-03 midg,1,midg; midg,igrid,midg 2.9986022E-02 -7.6230136E-03 1,midg,midg; igrid,midg,midg 8.9123175E-03 -1.0071509E-02 gauss-seidel spectral radius is 0.9986672 estimated iterations to convergence 217 setup time was (sec) 0.5400000 now iterating at: 09:12:50 rms-change max change #iterations 3.974967 187.1722 at 10iterations 1.876857 69.74534 at 20iterations 0.8886417 30.34764 at 30iterations 0.4204005 15.21801 at 40iterations 0.1988975 6.476471 at 50iterations 9.3730405E-02 3.093335 at 60iterations 4.4463031E-02 1.532593 at 70iterations 2.0871628E-02 0.6751766 at 80iterations 9.8917373E-03 0.3365555 at 90iterations 4.6904832E-03 0.1513648 at 100iterations 2.2144329E-03 7.7041626E-02 at 110iterations 1.0462118E-03 3.3697605E-02 at 120iterations finished qdiffx linear iterations at : 09:12:57 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 1.0462118E-03 3.3697605E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 09:12:57 7.736u 0.205s 0:08.24 96.2% 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 09:12:57 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.981075 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): -6.583000 35.04800 ymin,ymax (A): -4.261000 48.62000 zmin,zma (A): -23.64900 30.09000 x,y,z range (A): 41.63100 52.88100 53.73900 scale (grids/A): 2.981075 object centre (A): 14.23250 22.17950 3.220500 number of atom coordinates read : 2004 total number of charged atoms : 1871 net assigned charge : 1.000005 assigned positive charge : 296.8839 centred at (gu) : 94.67199 103.4281 91.15299 assigned negative charge : -295.8843 centred at (gu) : 95.18056 103.7582 90.87831 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 147136 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16986 grid for indexing accessible points = 1.400000 m= 78323 mr = 107012 m= 32273 mr = 65966 m= 8858 mr = 27411 m= 1614 mr = 7226 m= 157 mr = 1244 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 10006 time to turn everything in is 0.8500000 number of dielectric boundary points 59432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 14968 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) : 1.987383 object centre at (A) : 14.23250 22.17950 3.220500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7628694 -4.5566667E-02 midg,1,midg; midg,igrid,midg 0.2751166 -0.1297956 1,midg,midg; igrid,midg,midg 3.5795290E-02 -6.9563285E-02 gauss-seidel spectral radius is 0.9992553 estimated iterations to convergence 289 setup time was (sec) 1.090000 now iterating at: 09:12:59 rms-change max change #iterations 9.103869 432.6492 at 10iterations 5.224529 136.4960 at 20iterations 2.991506 63.43794 at 30iterations 1.716419 36.50201 at 40iterations 0.9813813 22.00578 at 50iterations 0.5610840 10.50161 at 60iterations 0.3216519 6.605444 at 70iterations 0.1835695 3.493325 at 80iterations 0.1052938 1.928528 at 90iterations 6.0158186E-02 1.306763 at 100iterations 3.4460265E-02 0.6511445 at 110iterations 1.9686798E-02 0.3596764 at 120iterations 1.1290394E-02 0.2323456 at 130iterations 6.4566936E-03 0.1202316 at 140iterations 3.7033008E-03 7.1600914E-02 at 150iterations 2.1175789E-03 3.7059784E-02 at 160iterations 1.2099777E-03 2.1543503E-02 at 170iterations 6.9413317E-04 1.2919426E-02 at 180iterations finished qdiffx linear iterations at : 09:13:10 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 6.9413317E-04 1.2919426E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 09:13:10 12.382u 0.189s 0:12.83 97.8% 0+0k 0+0io 0pf+0w