Sat Oct 8 11:43:39 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 8 2011 at 11:43:39 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4565 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: 0.5539563 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): -27.08400 35.11900 ymin,ymax (A): 34.95600 99.22100 zmin,zma (A): 31.12300 89.28100 x,y,z range (A): 62.20300 64.26500 58.15800 scale (grids/A): 0.5539563 object centre (A): 4.017500 67.08850 60.20200 number of atom coordinates read : 4565 total number of charged atoms : 4404 net assigned charge : -5.499951 assigned positive charge : 690.8215 centred at (gu) : 90.84829 87.95307 89.06107 assigned negative charge : -696.3253 centred at (gu) : 90.70697 88.04044 89.25211 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8814 nv = 96 ne = 84 npr = 96230 no. pairs analyzed = 96230 no. exposed pairs = 5101 no. arc points = 34877 no. surface atoms = 1722 nbur = 2843 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 = 1.540000 m= 364 mr = 5124 m= 0 mr = 23 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 144 time to turn everything in is 0.4400000 number of dielectric boundary points 4031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3587 ## 450 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11815 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6084379E-09 -2.5800886E-09 midg,1,midg; midg,igrid,midg 1.1358540E-09 -1.0707443E-09 1,midg,midg; igrid,midg,midg -2.0546960E-09 1.7305697E-09 gauss-seidel spectral radius is 0.9833018 estimated iterations to convergence 64 setup time was (sec) 0.7300000 now iterating at: 11:43:40 rms-change max change #iterations 0.1009060 14.13725 at 10iterations 7.3652603E-03 0.9217472 at 20iterations 7.9153141E-04 0.1001892 at 30iterations 1.8606290E-04 2.4247646E-02 at 40iterations 6.1110222E-05 8.3541870E-03 at 50iterations finished qdiffx linear iterations at : 11:43:44 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 6.1110222E-05 8.3541870E-03 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 11:43:44 4.503u 0.300s 0:05.09 94.3% 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 8 2011 at 11:43:44 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4565 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: 1.661869 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): -27.08400 35.11900 ymin,ymax (A): 34.95600 99.22100 zmin,zma (A): 31.12300 89.28100 x,y,z range (A): 62.20300 64.26500 58.15800 scale (grids/A): 1.661869 object centre (A): 4.017500 67.08850 60.20200 number of atom coordinates read : 4565 total number of charged atoms : 4404 net assigned charge : -5.499951 assigned positive charge : 690.8215 centred at (gu) : 92.54334 83.85786 87.18194 assigned negative charge : -696.3253 centred at (gu) : 92.12035 84.12082 87.75594 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 99643 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34877 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 32254 mr = 72397 m= 3776 mr = 23746 m= 101 mr = 2254 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 5898 time to turn everything in is 0.7100000 number of dielectric boundary points 37353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 381 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 33897 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) : 0.5539563 object centre at (A) : 4.017500 67.08850 60.20200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8207378E-02 -2.3166744E-02 midg,1,midg; midg,igrid,midg 2.1731615E-02 -3.1349643E-03 1,midg,midg; igrid,midg,midg -2.7575759E-02 2.2629401E-02 gauss-seidel spectral radius is 0.9983832 estimated iterations to convergence 197 setup time was (sec) 1.050000 now iterating at: 11:43:46 rms-change max change #iterations 4.446412 161.1593 at 10iterations 1.943682 66.35017 at 20iterations 0.8567165 24.16932 at 30iterations 0.3764864 10.94719 at 40iterations 0.1648828 4.842875 at 50iterations 7.2397023E-02 2.145271 at 60iterations 3.1928785E-02 0.8682237 at 70iterations 1.4018872E-02 0.4352493 at 80iterations 6.2073823E-03 0.1817818 at 90iterations 2.7584243E-03 8.0917358E-02 at 100iterations 1.2495994E-03 3.4996986E-02 at 110iterations 5.8407948E-04 1.9412756E-02 at 120iterations finished qdiffx linear iterations at : 11:43:54 total time elapsed so far: 9.810000 # loops : 120 mean,max change (kT/e) : 5.8407948E-04 1.9412756E-02 energy calculations done at 9.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.980000 DelPhi exited at 11:43:55 9.987u 0.260s 0:10.70 95.7% 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 Sat Oct 8 2011 at 11:43:55 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4565 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: 2.492803 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): -27.08400 35.11900 ymin,ymax (A): 34.95600 99.22100 zmin,zma (A): 31.12300 89.28100 x,y,z range (A): 62.20300 64.26500 58.15800 scale (grids/A): 2.492803 object centre (A): 4.017500 67.08850 60.20200 number of atom coordinates read : 4565 total number of charged atoms : 4404 net assigned charge : -5.499951 assigned positive charge : 690.8215 centred at (gu) : 93.81463 80.78652 85.77248 assigned negative charge : -696.3253 centred at (gu) : 93.18032 81.18108 86.63374 start vw surface at 0.1800000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 231876 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34877 grid for indexing accessible points = 1.400000 m= 111883 mr = 175862 m= 33530 mr = 92306 m= 6317 mr = 26612 m= 555 mr = 4739 m= 10 mr = 322 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 19424 time to turn everything in is 1.770000 number of dielectric boundary points 84330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 35207 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) : 1.661869 object centre at (A) : 4.017500 67.08850 60.20200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4880815 -0.2901930 midg,1,midg; midg,igrid,midg 0.3852205 0.1236541 1,midg,midg; igrid,midg,midg -0.3716516 0.2816397 gauss-seidel spectral radius is 0.9992156 estimated iterations to convergence 282 setup time was (sec) 2.130000 now iterating at: 11:43:58 rms-change max change #iterations 11.10770 360.4633 at 10iterations 6.372919 125.7551 at 20iterations 3.649436 70.46506 at 30iterations 2.085523 41.39420 at 40iterations 1.185621 20.71037 at 50iterations 0.6735893 10.93769 at 60iterations 0.3833559 6.208574 at 70iterations 0.2175775 3.759416 at 80iterations 0.1232717 2.129049 at 90iterations 6.9918968E-02 1.250546 at 100iterations 3.9610244E-02 0.6840477 at 110iterations 2.2415049E-02 0.3939285 at 120iterations 1.2737491E-02 0.2228470 at 130iterations 7.2208690E-03 0.1321871 at 140iterations 4.1142046E-03 6.5357208E-02 at 150iterations 2.3565339E-03 4.0325165E-02 at 160iterations 1.3576632E-03 2.3040771E-02 at 170iterations 7.9751556E-04 1.4160156E-02 at 180iterations finished qdiffx linear iterations at : 11:44:12 total time elapsed so far: 16.22000 # loops : 180 mean,max change (kT/e) : 7.9751556E-04 1.4160156E-02 energy calculations done at 16.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.39000 DelPhi exited at 11:44:12 16.394u 0.300s 0:16.96 98.4% 0+0k 0+0io 0pf+0w