Mon Oct 10 19:42:31 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 Mon Oct 10 2011 at 19:42:31 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 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: 0.6168882 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): 18.63400 65.21700 ymin,ymax (A): 11.80600 55.60100 zmin,zma (A): -1.002000 56.70700 x,y,z range (A): 46.58300 43.79500 57.70900 scale (grids/A): 0.6168882 object centre (A): 41.92550 33.70350 27.85250 number of atom coordinates read : 2385 total number of charged atoms : 2250 net assigned charge : 0.5000049 assigned positive charge : 345.4503 centred at (gu) : 91.26385 89.68502 89.45004 assigned negative charge : -344.9511 centred at (gu) : 91.21331 89.70118 89.47060 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5974 nv = 96 ne = 84 npr = 49149 no. pairs analyzed = 49149 no. exposed pairs = 2968 no. arc points = 21109 no. surface atoms = 1021 nbur = 1364 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 329 mr = 3203 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2122 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7401 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6080169E-09 -6.9892353E-10 midg,1,midg; midg,igrid,midg 1.2721409E-09 -5.1586579E-10 1,midg,midg; igrid,midg,midg -1.8202564E-09 4.0235641E-09 gauss-seidel spectral radius is 0.9863784 estimated iterations to convergence 70 setup time was (sec) 0.5400000 now iterating at: 19:42:32 rms-change max change #iterations 0.1138657 15.36124 at 10iterations 1.0590751E-02 1.786850 at 20iterations 9.9288940E-04 0.1342163 at 30iterations 9.5212396E-05 1.5663147E-02 at 40iterations 1.0586654E-05 1.6250610E-03 at 50iterations finished qdiffx linear iterations at : 19:42:35 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 1.0586654E-05 1.6250610E-03 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 19:42:36 4.207u 0.237s 0:04.88 90.7% 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 19:42:36 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.850665 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): 18.63400 65.21700 ymin,ymax (A): 11.80600 55.60100 zmin,zma (A): -1.002000 56.70700 x,y,z range (A): 46.58300 43.79500 57.70900 scale (grids/A): 1.850665 object centre (A): 41.92550 33.70350 27.85250 number of atom coordinates read : 2385 total number of charged atoms : 2250 net assigned charge : 0.5000049 assigned positive charge : 345.4503 centred at (gu) : 93.79134 89.05457 88.35002 assigned negative charge : -344.9511 centred at (gu) : 93.64013 89.10350 88.41193 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 65841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21109 grid for indexing accessible points = 1.400000 m= 22734 mr = 45080 m= 3491 mr = 16398 m= 174 mr = 2019 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 255 time to turn everything in is 0.6100000 number of dielectric boundary points 28692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17649 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) : 0.6168882 object centre at (A) : 41.92550 33.70350 27.85250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7972015E-02 -3.5980880E-02 midg,1,midg; midg,igrid,midg -5.6197876E-03 1.2497141E-03 1,midg,midg; igrid,midg,midg 1.6399860E-02 2.0544730E-02 gauss-seidel spectral radius is 0.9985398 estimated iterations to convergence 207 setup time was (sec) 0.9700000 now iterating at: 19:42:37 rms-change max change #iterations 3.772203 169.4625 at 10iterations 1.710295 64.63024 at 20iterations 0.7857113 28.52362 at 30iterations 0.3576447 14.20563 at 40iterations 0.1636200 5.413467 at 50iterations 7.4758366E-02 2.647184 at 60iterations 3.4115192E-02 1.110748 at 70iterations 1.5528897E-02 0.5260983 at 80iterations 7.1060723E-03 0.2458801 at 90iterations 3.2438447E-03 0.1136208 at 100iterations 1.4834683E-03 4.9301863E-02 at 110iterations 6.7878881E-04 2.2665024E-02 at 120iterations finished qdiffx linear iterations at : 19:42:46 total time elapsed so far: 9.570000 # loops : 120 mean,max change (kT/e) : 6.7878881E-04 2.2665024E-02 energy calculations done at 9.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.750000 DelPhi exited at 19:42:46 9.751u 0.280s 0:10.31 97.2% 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 19:42:46 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 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: 2.775997 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): 18.63400 65.21700 ymin,ymax (A): 11.80600 55.60100 zmin,zma (A): -1.002000 56.70700 x,y,z range (A): 46.58300 43.79500 57.70900 scale (grids/A): 2.775997 object centre (A): 41.92550 33.70350 27.85250 number of atom coordinates read : 2385 total number of charged atoms : 2250 net assigned charge : 0.5000049 assigned positive charge : 345.4503 centred at (gu) : 95.68698 88.58191 87.52496 assigned negative charge : -344.9511 centred at (gu) : 95.46021 88.65526 87.61803 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 152805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21109 grid for indexing accessible points = 1.400000 m= 73786 mr = 110039 m= 26402 mr = 59433 m= 5988 mr = 20830 m= 758 mr = 4308 m= 43 mr = 476 m= 0 mr = 9 time to grow re-entrant surface = 0.7400001 no. cavity mid-points inaccessible to solvent = 893 time to turn everything in is 1.350000 number of dielectric boundary points 64687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 17997 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) : 1.850665 object centre at (A) : 41.92550 33.70350 27.85250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4542985 -0.4549779 midg,1,midg; midg,igrid,midg -4.7628827E-02 -1.2731548E-02 1,midg,midg; igrid,midg,midg 0.2624664 0.2319656 gauss-seidel spectral radius is 0.9992300 estimated iterations to convergence 284 setup time was (sec) 1.700000 now iterating at: 19:42:48 rms-change max change #iterations 9.021723 310.7030 at 10iterations 5.261633 131.0261 at 20iterations 3.039583 72.17755 at 30iterations 1.751391 36.52859 at 40iterations 1.005708 19.93503 at 50iterations 0.5766358 11.35219 at 60iterations 0.3298886 6.463232 at 70iterations 0.1882194 3.987614 at 80iterations 0.1074109 2.076641 at 90iterations 6.1210681E-02 1.104256 at 100iterations 3.4901176E-02 0.7077780 at 110iterations 1.9875046E-02 0.4545784 at 120iterations 1.1309414E-02 0.2316113 at 130iterations 6.4582070E-03 0.1204634 at 140iterations 3.6683751E-03 6.9199562E-02 at 150iterations 2.0892855E-03 3.9739609E-02 at 160iterations 1.1944292E-03 2.2359014E-02 at 170iterations 6.8295759E-04 1.2519836E-02 at 180iterations finished qdiffx linear iterations at : 19:43:02 total time elapsed so far: 15.69000 # loops : 180 mean,max change (kT/e) : 6.8295759E-04 1.2519836E-02 energy calculations done at 15.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.87000 DelPhi exited at 19:43:03 15.869u 0.293s 0:16.44 98.2% 0+0k 0+0io 0pf+0w