Sat Oct 15 12:55:34 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 Sat Oct 15 2011 at 12:55:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2759 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: 0.6058956 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): -22.48600 36.27000 ymin,ymax (A): -26.63300 30.11700 zmin,zma (A): -5.614000 50.91200 x,y,z range (A): 58.75600 56.75000 56.52600 scale (grids/A): 0.6058956 object centre (A): 6.892000 1.742000 22.64900 number of atom coordinates read : 2759 total number of charged atoms : 2616 net assigned charge : -3.999980 assigned positive charge : 398.2153 centred at (gu) : 90.02734 93.25078 90.61895 assigned negative charge : -402.2167 centred at (gu) : 90.17872 93.14788 90.55006 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7099 nv = 96 ne = 84 npr = 54138 no. pairs analyzed = 54138 no. exposed pairs = 3773 no. arc points = 27182 no. surface atoms = 1274 nbur = 1485 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 375 mr = 3566 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2589 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8503 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6429194E-09 9.7904462E-10 midg,1,midg; midg,igrid,midg -3.3528105E-09 5.1447300E-09 1,midg,midg; igrid,midg,midg 4.4062913E-09 -9.1762749E-09 gauss-seidel spectral radius is 0.9859320 estimated iterations to convergence 69 setup time was (sec) 0.4000000 now iterating at: 12:55:35 rms-change max change #iterations 0.1130606 17.25288 at 10iterations 9.7437631E-03 1.559822 at 20iterations 9.0730056E-04 0.1422997 at 30iterations 1.2144799E-04 2.3365974E-02 at 40iterations 3.0073486E-05 6.4606667E-03 at 50iterations finished qdiffx linear iterations at : 12:55:38 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 3.0073486E-05 6.4606667E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 12:55:38 3.489u 0.208s 0:03.96 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 Sat Oct 15 2011 at 12:55:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2759 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: 1.817687 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): -22.48600 36.27000 ymin,ymax (A): -26.63300 30.11700 zmin,zma (A): -5.614000 50.91200 x,y,z range (A): 58.75600 56.75000 56.52600 scale (grids/A): 1.817687 object centre (A): 6.892000 1.742000 22.64900 number of atom coordinates read : 2759 total number of charged atoms : 2616 net assigned charge : -3.999980 assigned positive charge : 398.2153 centred at (gu) : 90.08152 99.75154 91.85614 assigned negative charge : -402.2167 centred at (gu) : 90.53632 99.44363 91.65030 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27182 grid for indexing accessible points = 1.400000 m= 25713 mr = 50793 m= 3776 mr = 17748 m= 240 mr = 2137 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 35838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20445 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) : 0.6058956 object centre at (A) : 6.892000 1.742000 22.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3357577E-03 2.9265324E-02 midg,1,midg; midg,igrid,midg -2.4088193E-02 2.8006352E-02 1,midg,midg; igrid,midg,midg -1.4943789E-02 -3.5099581E-02 gauss-seidel spectral radius is 0.9985416 estimated iterations to convergence 208 setup time was (sec) 0.6100000 now iterating at: 12:55:39 rms-change max change #iterations 3.947533 175.6476 at 10iterations 1.785814 61.88506 at 20iterations 0.8123152 27.36044 at 30iterations 0.3702392 12.24706 at 40iterations 0.1683977 6.085069 at 50iterations 7.6996148E-02 2.947973 at 60iterations 3.5045780E-02 1.129076 at 70iterations 1.5998878E-02 0.6197510 at 80iterations 7.3050619E-03 0.2425957 at 90iterations 3.3424187E-03 0.1219444 at 100iterations 1.5389754E-03 4.8504829E-02 at 110iterations 7.0929714E-04 2.2129059E-02 at 120iterations finished qdiffx linear iterations at : 12:55:46 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 7.0929714E-04 2.2129059E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 12:55:47 8.128u 0.256s 0:08.89 94.1% 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 Sat Oct 15 2011 at 12:55:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2759 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: 2.726530 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): -22.48600 36.27000 ymin,ymax (A): -26.63300 30.11700 zmin,zma (A): -5.614000 50.91200 x,y,z range (A): 58.75600 56.75000 56.52600 scale (grids/A): 2.726530 object centre (A): 6.892000 1.742000 22.64900 number of atom coordinates read : 2759 total number of charged atoms : 2616 net assigned charge : -3.999980 assigned positive charge : 398.2153 centred at (gu) : 90.12206 104.6273 92.78403 assigned negative charge : -402.2167 centred at (gu) : 90.80434 104.1654 92.47539 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 177901 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27182 grid for indexing accessible points = 1.400000 m= 84206 mr = 124334 m= 28739 mr = 66128 m= 6549 mr = 22040 m= 932 mr = 4565 m= 55 mr = 561 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 80738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 20923 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) : 1.817687 object centre at (A) : 6.892000 1.742000 22.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7172226E-02 0.3872298 midg,1,midg; midg,igrid,midg -0.2929701 0.3612916 1,midg,midg; igrid,midg,midg -0.2967497 -0.2884901 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 1.220000 now iterating at: 12:55:48 rms-change max change #iterations 9.595922 291.7697 at 10iterations 5.623363 133.9634 at 20iterations 3.270328 74.26518 at 30iterations 1.893904 39.61321 at 40iterations 1.089433 20.67083 at 50iterations 0.6277528 12.47968 at 60iterations 0.3601890 6.587747 at 70iterations 0.2065948 4.024574 at 80iterations 0.1183907 2.284867 at 90iterations 6.7763612E-02 1.314877 at 100iterations 3.8717572E-02 0.7067947 at 110iterations 2.2103822E-02 0.4221115 at 120iterations 1.2661771E-02 0.2275391 at 130iterations 7.2425231E-03 0.1292877 at 140iterations 4.1548940E-03 7.7839851E-02 at 150iterations 2.3907514E-03 4.4533730E-02 at 160iterations 1.3795284E-03 2.6568294E-02 at 170iterations 8.0300728E-04 1.8242836E-02 at 180iterations finished qdiffx linear iterations at : 12:56:01 total time elapsed so far: 13.30000 # loops : 180 mean,max change (kT/e) : 8.0300728E-04 1.8242836E-02 energy calculations done at 13.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 12:56:01 13.433u 0.286s 0:14.06 97.5% 0+0k 0+0io 0pf+0w