Mon Oct 10 17:14:35 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 17:14:35 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3186 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: 0.5991955 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): -8.971000 48.39000 ymin,ymax (A): -8.699000 43.98300 zmin,zma (A): -4.404000 55.00900 x,y,z range (A): 57.36100 52.68200 59.41300 scale (grids/A): 0.5991955 object centre (A): 19.70950 17.64200 25.30250 number of atom coordinates read : 3186 total number of charged atoms : 3044 net assigned charge : -2.999965 assigned positive charge : 480.2466 centred at (gu) : 89.58451 88.63110 89.13894 assigned negative charge : -483.2479 centred at (gu) : 89.53829 88.52955 89.02120 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7560 nv = 96 ne = 84 npr = 64262 no. pairs analyzed = 64262 no. exposed pairs = 4235 no. arc points = 29288 no. surface atoms = 1436 nbur = 1750 mkacc time = 0.2100000 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 = 1.456000 m= 348 mr = 3887 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 41 time to turn everything in is 0.4600000 number of dielectric boundary points 3993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3011 ## 312 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.7874329E-09 3.2836351E-09 midg,1,midg; midg,igrid,midg -7.7537834E-09 2.4095324E-09 1,midg,midg; igrid,midg,midg -3.4795102E-09 8.2732426E-10 gauss-seidel spectral radius is 0.9856393 estimated iterations to convergence 68 setup time was (sec) 0.7600000 now iterating at: 17:14:36 rms-change max change #iterations 0.1202297 17.91325 at 10iterations 1.0252326E-02 1.574508 at 20iterations 8.6117291E-04 0.1385279 at 30iterations 7.6273413E-05 9.6874237E-03 at 40iterations 8.3528357E-06 1.3961792E-03 at 50iterations finished qdiffx linear iterations at : 17:14:40 total time elapsed so far: 4.580000 # loops : 50 mean,max change (kT/e) : 8.3528357E-06 1.3961792E-03 energy calculations done at 4.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.790000 DelPhi exited at 17:14:41 4.796u 0.463s 0:05.69 92.2% 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 17:14:41 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3186 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: 1.797586 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): -8.971000 48.39000 ymin,ymax (A): -8.699000 43.98300 zmin,zma (A): -4.404000 55.00900 x,y,z range (A): 57.36100 52.68200 59.41300 scale (grids/A): 1.797586 object centre (A): 19.70950 17.64200 25.30250 number of atom coordinates read : 3186 total number of charged atoms : 3044 net assigned charge : -2.999965 assigned positive charge : 480.2466 centred at (gu) : 88.75259 85.89262 87.41575 assigned negative charge : -483.2479 centred at (gu) : 88.61435 85.58825 87.06319 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 82595 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29288 grid for indexing accessible points = 1.400000 m= 27127 mr = 55670 m= 3345 mr = 18761 m= 140 mr = 1690 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 600 time to turn everything in is 0.8300000 number of dielectric boundary points 37062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 244 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 23766 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) : 0.5991955 object centre at (A) : 19.70950 17.64200 25.30250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9046368E-03 1.8620495E-02 midg,1,midg; midg,igrid,midg -3.3730395E-02 4.8248242E-03 1,midg,midg; igrid,midg,midg -3.8753934E-02 1.9463297E-02 gauss-seidel spectral radius is 0.9985330 estimated iterations to convergence 207 setup time was (sec) 1.170000 now iterating at: 17:14:43 rms-change max change #iterations 4.227615 196.1696 at 10iterations 1.914535 66.19259 at 20iterations 0.8703263 28.88936 at 30iterations 0.3940821 12.39083 at 40iterations 0.1799042 5.710697 at 50iterations 8.1836917E-02 2.679092 at 60iterations 3.7157755E-02 1.171834 at 70iterations 1.6935160E-02 0.5156555 at 80iterations 7.7081495E-03 0.2499619 at 90iterations 3.5094514E-03 0.1082122 at 100iterations 1.5923341E-03 5.2401960E-02 at 110iterations 7.2601368E-04 2.4890900E-02 at 120iterations finished qdiffx linear iterations at : 17:14:53 total time elapsed so far: 11.02000 # loops : 120 mean,max change (kT/e) : 7.2601368E-04 2.4890900E-02 energy calculations done at 11.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.23000 DelPhi exited at 17:14:53 11.233u 0.555s 0:12.13 97.1% 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 17:14:53 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3186 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: 2.696380 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): -8.971000 48.39000 ymin,ymax (A): -8.699000 43.98300 zmin,zma (A): -4.404000 55.00900 x,y,z range (A): 57.36100 52.68200 59.41300 scale (grids/A): 2.696380 object centre (A): 19.70950 17.64200 25.30250 number of atom coordinates read : 3186 total number of charged atoms : 3044 net assigned charge : -2.999965 assigned positive charge : 480.2466 centred at (gu) : 88.12877 83.83867 86.12316 assigned negative charge : -483.2479 centred at (gu) : 87.92137 83.38200 85.59470 start vw surface at 0.1600000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 191315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29288 grid for indexing accessible points = 1.400000 m= 90822 mr = 135904 m= 28758 mr = 71812 m= 5604 mr = 21737 m= 556 mr = 3673 m= 19 mr = 277 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 2063 time to turn everything in is 2.140000 number of dielectric boundary points 83668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 24347 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) : 1.797586 object centre at (A) : 19.70950 17.64200 25.30250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2007534 0.1557976 midg,1,midg; midg,igrid,midg -0.3698457 6.7352451E-02 1,midg,midg; igrid,midg,midg -0.4809973 0.3558974 gauss-seidel spectral radius is 0.9992533 estimated iterations to convergence 289 setup time was (sec) 2.510000 now iterating at: 17:14:56 rms-change max change #iterations 10.52243 353.5580 at 10iterations 6.215814 160.2845 at 20iterations 3.622868 74.60637 at 30iterations 2.107282 43.45942 at 40iterations 1.221982 24.59490 at 50iterations 0.7068251 16.15041 at 60iterations 0.4080486 7.417206 at 70iterations 0.2348050 4.022800 at 80iterations 0.1348673 2.733332 at 90iterations 7.7582538E-02 1.445559 at 100iterations 4.4560872E-02 0.8595123 at 110iterations 2.5553085E-02 0.4930239 at 120iterations 1.4640924E-02 0.2854390 at 130iterations 8.3953775E-03 0.1476541 at 140iterations 4.8136264E-03 8.5824966E-02 at 150iterations 2.7572762E-03 4.7327936E-02 at 160iterations 1.5834626E-03 3.0817032E-02 at 170iterations 9.0630900E-04 1.5647888E-02 at 180iterations finished qdiffx linear iterations at : 17:15:13 total time elapsed so far: 19.37000 # loops : 180 mean,max change (kT/e) : 9.0630900E-04 1.5647888E-02 energy calculations done at 19.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.59000 DelPhi exited at 17:15:14 19.595u 0.549s 0:20.88 96.4% 0+0k 0+0io 0pf+0w