Mon Oct 10 10:34:21 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 10:34:21 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 = 2912 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5491369 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): -21.10700 43.72200 ymin,ymax (A): -11.28900 45.97500 zmin,zma (A): -1.979000 51.37200 x,y,z range (A): 64.82900 57.26400 53.35100 scale (grids/A): 0.5491369 object centre (A): 11.30750 17.34300 24.69650 number of atom coordinates read : 2912 total number of charged atoms : 2759 net assigned charge : 6.000015 assigned positive charge : 425.8538 centred at (gu) : 91.57791 91.07108 86.73520 assigned negative charge : -419.8542 centred at (gu) : 91.62411 91.16686 86.55938 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5872 nv = 96 ne = 84 npr = 56778 no. pairs analyzed = 56778 no. exposed pairs = 4357 no. arc points = 31647 no. surface atoms = 1452 nbur = 1460 mkacc time = 0.1300000 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 = 1.540000 m= 241 mr = 2505 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3602 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3052 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7532 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8072472E-09 7.5366169E-10 midg,1,midg; midg,igrid,midg 8.6871571E-10 -2.6264912E-10 1,midg,midg; igrid,midg,midg 5.4077248E-10 2.1718675E-10 gauss-seidel spectral radius is 0.9829126 estimated iterations to convergence 63 setup time was (sec) 0.5800000 now iterating at: 10:34:21 rms-change max change #iterations 7.0071772E-02 17.34265 at 10iterations 4.7453423E-03 0.7636414 at 20iterations 3.9249894E-04 6.9488525E-02 at 30iterations 5.1693292E-05 9.5176697E-03 at 40iterations 9.9137715E-06 1.6174316E-03 at 50iterations finished qdiffx linear iterations at : 10:34:25 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 9.9137715E-06 1.6174316E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 10:34:25 4.243u 0.236s 0:04.75 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 Mon Oct 10 2011 at 10:34:25 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 = 2912 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: 1.647411 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): -21.10700 43.72200 ymin,ymax (A): -11.28900 45.97500 zmin,zma (A): -1.979000 51.37200 x,y,z range (A): 64.82900 57.26400 53.35100 scale (grids/A): 1.647411 object centre (A): 11.30750 17.34300 24.69650 number of atom coordinates read : 2912 total number of charged atoms : 2759 net assigned charge : 6.000015 assigned positive charge : 425.8538 centred at (gu) : 94.73322 93.21325 80.20493 assigned negative charge : -419.8542 centred at (gu) : 94.87212 93.50025 79.67781 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63350 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31647 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18612 mr = 38408 m= 1864 mr = 11479 m= 56 mr = 713 m= 0 mr = 1 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.5000000 number of dielectric boundary points 33281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 21162 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) : 0.5491369 object centre at (A) : 11.30750 17.34300 24.69650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1198028E-03 8.1024794E-03 midg,1,midg; midg,igrid,midg 1.6577778E-02 4.2623361E-03 1,midg,midg; igrid,midg,midg -1.2869813E-02 -1.5538726E-02 gauss-seidel spectral radius is 0.9982256 estimated iterations to convergence 189 setup time was (sec) 0.8400000 now iterating at: 10:34:27 rms-change max change #iterations 3.255177 151.4330 at 10iterations 1.362892 51.50804 at 20iterations 0.5698538 21.36062 at 30iterations 0.2387492 9.231199 at 40iterations 0.1002326 3.803524 at 50iterations 4.2121422E-02 1.487998 at 60iterations 1.7670318E-02 0.6558189 at 70iterations 7.4278708E-03 0.3156719 at 80iterations 3.1230012E-03 0.1148992 at 90iterations 1.3199779E-03 4.6035767E-02 at 100iterations 5.5892207E-04 2.4494171E-02 at 110iterations 2.3825957E-04 9.1896057E-03 at 120iterations finished qdiffx linear iterations at : 10:34:35 total time elapsed so far: 9.510000 # loops : 120 mean,max change (kT/e) : 2.3825957E-04 9.1896057E-03 energy calculations done at 9.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.700000 DelPhi exited at 10:34:36 9.700u 0.263s 0:10.29 96.7% 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 10:34:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2912 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.471116 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): -21.10700 43.72200 ymin,ymax (A): -11.28900 45.97500 zmin,zma (A): -1.979000 51.37200 x,y,z range (A): 64.82900 57.26400 53.35100 scale (grids/A): 2.471116 object centre (A): 11.30750 17.34300 24.69650 number of atom coordinates read : 2912 total number of charged atoms : 2759 net assigned charge : 6.000015 assigned positive charge : 425.8538 centred at (gu) : 97.09985 94.81969 75.30733 assigned negative charge : -419.8542 centred at (gu) : 97.30817 95.25038 74.51670 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 146762 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31647 grid for indexing accessible points = 1.400000 m= 63120 mr = 95174 m= 18106 mr = 46529 m= 2663 mr = 12458 m= 162 mr = 1440 m= 0 mr = 46 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 66 time to turn everything in is 1.190000 number of dielectric boundary points 75166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 22045 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) : 1.647411 object centre at (A) : 11.30750 17.34300 24.69650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4260900E-02 0.1046057 midg,1,midg; midg,igrid,midg 0.3280362 -4.5804284E-03 1,midg,midg; igrid,midg,midg -0.6247467 -0.5253379 gauss-seidel spectral radius is 0.9991596 estimated iterations to convergence 272 setup time was (sec) 1.530000 now iterating at: 10:34:38 rms-change max change #iterations 8.808731 362.0158 at 10iterations 5.109621 181.1070 at 20iterations 2.922741 103.1977 at 30iterations 1.660909 52.92860 at 40iterations 0.9367341 26.63708 at 50iterations 0.5241028 13.52782 at 60iterations 0.2934794 7.387669 at 70iterations 0.1641487 4.514557 at 80iterations 9.1393337E-02 2.454813 at 90iterations 5.0853666E-02 1.164546 at 100iterations 2.8202472E-02 0.7119141 at 110iterations 1.5656317E-02 0.3335724 at 120iterations 8.6848736E-03 0.2203612 at 130iterations 4.8216651E-03 0.1029263 at 140iterations 2.6713719E-03 6.5961599E-02 at 150iterations 1.4831683E-03 3.4413576E-02 at 160iterations 8.2054880E-04 1.8651009E-02 at 170iterations 4.5595135E-04 9.1381073E-03 at 180iterations finished qdiffx linear iterations at : 10:34:51 total time elapsed so far: 15.31000 # loops : 180 mean,max change (kT/e) : 4.5595135E-04 9.1381073E-03 energy calculations done at 15.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.49000 DelPhi exited at 10:34:52 15.490u 0.302s 0:16.10 98.0% 0+0k 0+0io 0pf+0w