Sun Oct 9 04:30:15 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 Sun Oct 9 2011 at 04:30:15 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 = 4016 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5612575 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): 36.32000 80.99100 ymin,ymax (A): 50.00700 113.3880 zmin,zma (A): -20.37500 43.05400 x,y,z range (A): 44.67101 63.38100 63.42900 scale (grids/A): 0.5612575 object centre (A): 58.65550 81.69750 11.33950 number of atom coordinates read : 4016 total number of charged atoms : 3870 net assigned charge : 2.000014 assigned positive charge : 583.7092 centred at (gu) : 89.74510 89.03509 90.93683 assigned negative charge : -581.7117 centred at (gu) : 89.73341 88.89262 91.03320 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8350 nv = 96 ne = 84 npr = 81654 no. pairs analyzed = 81654 no. exposed pairs = 5456 no. arc points = 37406 no. surface atoms = 1834 nbur = 2182 mkacc time = 0.1700000 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= 383 mr = 4270 m= 0 mr = 19 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 4444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3643 ## 400 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10800 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3580392E-09 -1.5298761E-09 midg,1,midg; midg,igrid,midg -2.4526272E-09 1.8841777E-09 1,midg,midg; igrid,midg,midg 9.1694916E-11 4.1458398E-10 gauss-seidel spectral radius is 0.9837123 estimated iterations to convergence 64 setup time was (sec) 0.6200000 now iterating at: 04:30:16 rms-change max change #iterations 9.6768677E-02 14.60482 at 10iterations 7.5748567E-03 1.051424 at 20iterations 1.3577883E-03 0.1986842 at 30iterations 6.3623057E-04 0.1000838 at 40iterations 3.2827116E-04 5.3079605E-02 at 50iterations finished qdiffx linear iterations at : 04:30:18 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 3.2827116E-04 5.3079605E-02 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 04:30:19 3.203u 0.162s 0:03.68 91.3% 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 Sun Oct 9 2011 at 04:30:19 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 = 4016 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.683772 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): 36.32000 80.99100 ymin,ymax (A): 50.00700 113.3880 zmin,zma (A): -20.37500 43.05400 x,y,z range (A): 44.67101 63.38100 63.42900 scale (grids/A): 1.683772 object centre (A): 58.65550 81.69750 11.33950 number of atom coordinates read : 4016 total number of charged atoms : 3870 net assigned charge : 2.000014 assigned positive charge : 583.7092 centred at (gu) : 89.23389 87.10415 92.80894 assigned negative charge : -581.7117 centred at (gu) : 89.20013 86.67783 93.09933 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 90880 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37406 grid for indexing accessible points = 1.400000 m= 31343 mr = 61256 m= 4306 mr = 21744 m= 173 mr = 2397 m= 2 mr = 19 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 0.6300000 number of dielectric boundary points 41288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 325 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 29896 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) : 0.5612575 object centre at (A) : 58.65550 81.69750 11.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3588173E-02 3.5602732E-03 midg,1,midg; midg,igrid,midg -4.7628503E-02 5.4680434E-04 1,midg,midg; igrid,midg,midg 9.6619381E-03 -2.5578835E-03 gauss-seidel spectral radius is 0.9984146 estimated iterations to convergence 199 setup time was (sec) 0.8900000 now iterating at: 04:30:20 rms-change max change #iterations 4.167340 152.1376 at 10iterations 1.847308 53.65519 at 20iterations 0.8141250 25.32631 at 30iterations 0.3597278 14.21292 at 40iterations 0.1590655 4.749031 at 50iterations 7.0861742E-02 2.538815 at 60iterations 3.1393055E-02 1.074669 at 70iterations 1.4099799E-02 0.4561410 at 80iterations 6.4898850E-03 0.2074528 at 90iterations 3.1943489E-03 0.1138787 at 100iterations 1.8125568E-03 6.3639164E-02 at 110iterations 1.1937199E-03 4.2692184E-02 at 120iterations finished qdiffx linear iterations at : 04:30:26 total time elapsed so far: 6.980000 # loops : 120 mean,max change (kT/e) : 1.1937199E-03 4.2692184E-02 energy calculations done at 6.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 04:30:26 7.154u 0.198s 0:07.64 96.0% 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 Sun Oct 9 2011 at 04:30:26 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 = 4016 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.525659 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): 36.32000 80.99100 ymin,ymax (A): 50.00700 113.3880 zmin,zma (A): -20.37500 43.05400 x,y,z range (A): 44.67101 63.38100 63.42900 scale (grids/A): 2.525659 object centre (A): 58.65550 81.69750 11.33950 number of atom coordinates read : 4016 total number of charged atoms : 3870 net assigned charge : 2.000014 assigned positive charge : 583.7092 centred at (gu) : 88.85078 85.65585 94.21318 assigned negative charge : -581.7117 centred at (gu) : 88.80000 85.01655 94.64893 start vw surface at 0.1800000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 210525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37406 grid for indexing accessible points = 1.400000 m= 102674 mr = 150080 m= 34768 mr = 80512 m= 7337 mr = 26666 m= 700 mr = 5127 m= 11 mr = 350 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.570000 number of dielectric boundary points 93280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 30923 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) : 1.683772 object centre at (A) : 58.65550 81.69750 11.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5334979 -0.1207189 midg,1,midg; midg,igrid,midg -0.8022407 -4.2950753E-02 1,midg,midg; igrid,midg,midg 0.1674988 -4.0259451E-02 gauss-seidel spectral radius is 0.9992445 estimated iterations to convergence 287 setup time was (sec) 1.860000 now iterating at: 04:30:28 rms-change max change #iterations 10.83863 341.5367 at 10iterations 6.437248 146.6101 at 20iterations 3.800593 73.19133 at 30iterations 2.220237 43.81779 at 40iterations 1.291859 26.47491 at 50iterations 0.7495843 13.62661 at 60iterations 0.4336809 10.36338 at 70iterations 0.2504579 4.316132 at 80iterations 0.1444034 2.851119 at 90iterations 8.2804970E-02 1.534149 at 100iterations 4.7648735E-02 0.9130478 at 110iterations 2.7437491E-02 0.5194168 at 120iterations 1.5787879E-02 0.2738619 at 130iterations 9.1708703E-03 0.1773324 at 140iterations 5.3754514E-03 9.5673561E-02 at 150iterations 3.2349215E-03 5.8704376E-02 at 160iterations 2.0400097E-03 4.1136742E-02 at 170iterations 1.3770103E-03 2.7078629E-02 at 180iterations finished qdiffx linear iterations at : 04:30:38 total time elapsed so far: 11.68000 # loops : 180 mean,max change (kT/e) : 1.3770103E-03 2.7078629E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.86000 DelPhi exited at 04:30:39 11.867u 0.187s 0:12.32 97.7% 0+0k 0+0io 0pf+0w