Sat Oct 15 14:00:03 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 Sat Oct 15 2011 at 14:00:05 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: 389 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4333 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5095541 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): -15.72000 37.33500 ymin,ymax (A): -32.58800 31.54600 zmin,zma (A): -3.816000 66.04900 x,y,z range (A): 53.05500 64.13400 69.86501 scale (grids/A): 0.5095541 object centre (A): 10.80750 -0.5210009 31.11650 number of atom coordinates read : 4333 total number of charged atoms : 4127 net assigned charge : -0.1939719 assigned positive charge : 649.2762 centred at (gu) : 89.91157 90.88210 87.50822 assigned negative charge : -649.4743 centred at (gu) : 89.79875 90.95195 87.62438 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7110 nv = 96 ne = 84 npr = 87903 no. pairs analyzed = 87903 no. exposed pairs = 5735 no. arc points = 39936 no. surface atoms = 1897 nbur = 2436 mkacc time = 0.2500000 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 = 1.680000 m= 280 mr = 3579 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 3803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3862 ## 597 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 9573 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8871190E-10 -1.4059511E-10 midg,1,midg; midg,igrid,midg 1.1617426E-10 -2.0978309E-10 1,midg,midg; igrid,midg,midg -2.7020639E-10 2.3511898E-10 gauss-seidel spectral radius is 0.9802737 estimated iterations to convergence 59 setup time was (sec) 0.8400000 now iterating at: 14:00:07 rms-change max change #iterations 6.4566389E-02 9.701303 at 10iterations 3.7087656E-03 0.6698034 at 20iterations 2.2856335E-04 3.4900665E-02 at 30iterations 2.8168626E-05 5.7201385E-03 at 40iterations 6.5943073E-06 1.0414124E-03 at 50iterations finished qdiffx linear iterations at : 14:00:19 total time elapsed so far: 5.520000 # loops : 50 mean,max change (kT/e) : 6.5943073E-06 1.0414124E-03 energy calculations done at 5.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.680000 DelPhi exited at 14:00:20 5.685u 0.505s 0:15.71 39.3% 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 Sat Oct 15 2011 at 14:00:22 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: 389 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4333 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.528662 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): -15.72000 37.33500 ymin,ymax (A): -32.58800 31.54600 zmin,zma (A): -3.816000 66.04900 x,y,z range (A): 53.05500 64.13400 69.86501 scale (grids/A): 1.528662 object centre (A): 10.80750 -0.5210009 31.11650 number of atom coordinates read : 4333 total number of charged atoms : 4127 net assigned charge : -0.1939719 assigned positive charge : 649.2762 centred at (gu) : 89.73369 92.64513 82.52352 assigned negative charge : -649.4743 centred at (gu) : 89.39607 92.85544 82.87301 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 79496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39936 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22837 mr = 53274 m= 2035 mr = 14833 m= 41 mr = 844 m= 0 mr = 4 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 333 time to turn everything in is 0.7100000 number of dielectric boundary points 35454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 521 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 31051 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) : 0.5095541 object centre at (A) : 10.80750 -0.5210009 31.11650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6752519E-03 -1.3332328E-02 midg,1,midg; midg,igrid,midg -1.4294478E-03 -1.3505230E-02 1,midg,midg; igrid,midg,midg -2.1474753E-03 8.5464921E-03 gauss-seidel spectral radius is 0.9980617 estimated iterations to convergence 181 setup time was (sec) 1.080000 now iterating at: 14:00:25 rms-change max change #iterations 3.579847 149.9686 at 10iterations 1.439257 53.16125 at 20iterations 0.5825028 18.89112 at 30iterations 0.2369642 7.957383 at 40iterations 9.5564954E-02 3.419075 at 50iterations 3.8671520E-02 1.514740 at 60iterations 1.5728455E-02 0.5678825 at 70iterations 6.3857860E-03 0.2148533 at 80iterations 2.5989099E-03 9.2365265E-02 at 90iterations 1.0540438E-03 3.3973694E-02 at 100iterations 4.3296488E-04 1.5958309E-02 at 110iterations 1.8007419E-04 6.4182281E-03 at 120iterations finished qdiffx linear iterations at : 14:00:53 total time elapsed so far: 12.81000 # loops : 120 mean,max change (kT/e) : 1.8007419E-04 6.4182281E-03 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 14:00:55 12.993u 0.518s 0:33.22 40.6% 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 Sat Oct 15 2011 at 14:00:57 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: 389 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4333 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.292994 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): -15.72000 37.33500 ymin,ymax (A): -32.58800 31.54600 zmin,zma (A): -3.816000 66.04900 x,y,z range (A): 53.05500 64.13400 69.86501 scale (grids/A): 2.292994 object centre (A): 10.80750 -0.5210009 31.11650 number of atom coordinates read : 4333 total number of charged atoms : 4127 net assigned charge : -0.1939719 assigned positive charge : 649.2762 centred at (gu) : 89.60027 93.96739 78.78510 assigned negative charge : -649.4743 centred at (gu) : 89.09388 94.28307 79.30930 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 185225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39936 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 80953 mr = 131149 m= 20434 mr = 62094 m= 2859 mr = 14417 m= 144 mr = 1733 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 1155 time to turn everything in is 1.730000 number of dielectric boundary points 80166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 32913 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) : 1.528662 object centre at (A) : 10.80750 -0.5210009 31.11650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1604299 -0.2821063 midg,1,midg; midg,igrid,midg -8.0284975E-02 -0.2885774 1,midg,midg; igrid,midg,midg -3.0056057E-02 0.1328284 gauss-seidel spectral radius is 0.9991387 estimated iterations to convergence 269 setup time was (sec) 2.130000 now iterating at: 14:01:07 rms-change max change #iterations 9.680110 261.9514 at 10iterations 5.496298 147.2899 at 20iterations 3.093513 73.16512 at 30iterations 1.739676 41.30395 at 40iterations 0.9720600 20.56010 at 50iterations 0.5411990 12.70164 at 60iterations 0.3009834 7.305574 at 70iterations 0.1668462 3.925755 at 80iterations 9.2441685E-02 2.034132 at 90iterations 5.1129580E-02 1.096928 at 100iterations 2.8254196E-02 0.5702567 at 110iterations 1.5610319E-02 0.3278375 at 120iterations 8.6305058E-03 0.1948340 at 130iterations 4.7551822E-03 9.6414804E-02 at 140iterations 2.6192649E-03 5.4543972E-02 at 150iterations 1.4478188E-03 2.9731750E-02 at 160iterations 7.9768972E-04 1.5308380E-02 at 170iterations 4.4142065E-04 9.7961426E-03 at 180iterations finished qdiffx linear iterations at : 14:02:02 total time elapsed so far: 22.31000 # loops : 180 mean,max change (kT/e) : 4.4142065E-04 9.7961426E-03 energy calculations done at 22.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.48000 DelPhi exited at 14:02:03 22.483u 0.584s 1:06.19 34.8% 0+0k 0+0io 0pf+0w