Tue Oct 11 07:19:46 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 Tue Oct 11 2011 at 07:19:46 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3169 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5964348 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): 0.1320000 48.45000 ymin,ymax (A): -8.090000 48.85500 zmin,zma (A): 0.9669999 60.65500 x,y,z range (A): 48.31800 56.94500 59.68800 scale (grids/A): 0.5964348 object centre (A): 24.29100 20.38250 30.81100 number of atom coordinates read : 3169 total number of charged atoms : 3018 net assigned charge : -1.099989 assigned positive charge : 473.7659 centred at (gu) : 89.50335 89.36140 91.06750 assigned negative charge : -474.8670 centred at (gu) : 89.39160 89.28134 90.99214 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7357 nv = 96 ne = 84 npr = 65778 no. pairs analyzed = 65778 no. exposed pairs = 3639 no. arc points = 24638 no. surface atoms = 1249 nbur = 1920 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 4282 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3400000 number of dielectric boundary points 3370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2470 ## 249 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9264 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6875762E-09 3.3162775E-09 midg,1,midg; midg,igrid,midg -4.2046406E-09 2.3797575E-09 1,midg,midg; igrid,midg,midg -5.5196456E-09 3.5617038E-09 gauss-seidel spectral radius is 0.9854934 estimated iterations to convergence 68 setup time was (sec) 0.5800000 now iterating at: 07:19:47 rms-change max change #iterations 0.1197387 19.04971 at 10iterations 1.0650930E-02 1.427555 at 20iterations 1.2224416E-03 0.1874771 at 30iterations 2.8916320E-04 4.8503876E-02 at 40iterations 8.3595580E-05 1.4329910E-02 at 50iterations finished qdiffx linear iterations at : 07:19:50 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 8.3595580E-05 1.4329910E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 07:19:50 3.446u 0.189s 0:03.91 92.5% 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 Tue Oct 11 2011 at 07:19:50 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3169 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.789304 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): 0.1320000 48.45000 ymin,ymax (A): -8.090000 48.85500 zmin,zma (A): 0.9669999 60.65500 x,y,z range (A): 48.31800 56.94500 59.68800 scale (grids/A): 1.789304 object centre (A): 24.29100 20.38250 30.81100 number of atom coordinates read : 3169 total number of charged atoms : 3018 net assigned charge : -1.099989 assigned positive charge : 473.7659 centred at (gu) : 88.50943 88.08327 93.20185 assigned negative charge : -474.8670 centred at (gu) : 88.17418 87.84351 92.97591 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24638 grid for indexing accessible points = 1.400000 m= 29085 mr = 58458 m= 3664 mr = 22120 m= 142 mr = 2225 m= 4 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1328 time to turn everything in is 0.5700000 number of dielectric boundary points 31257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 205 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 23543 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) : 0.5964348 object centre at (A) : 24.29100 20.38250 30.81100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9655647E-02 2.5662170E-03 midg,1,midg; midg,igrid,midg -2.4297163E-02 6.8173734E-03 1,midg,midg; igrid,midg,midg -1.4264226E-02 1.0674408E-02 gauss-seidel spectral radius is 0.9985085 estimated iterations to convergence 205 setup time was (sec) 0.8600000 now iterating at: 07:19:51 rms-change max change #iterations 4.213175 155.2410 at 10iterations 1.911658 64.65414 at 20iterations 0.8682299 32.14494 at 30iterations 0.3940318 13.05360 at 40iterations 0.1794805 5.811591 at 50iterations 8.1541307E-02 2.828964 at 60iterations 3.7095413E-02 1.169025 at 70iterations 1.6921526E-02 0.5137482 at 80iterations 7.7178655E-03 0.2411680 at 90iterations 3.5726274E-03 0.1163836 at 100iterations 1.6861729E-03 5.2877426E-02 at 110iterations 8.1403705E-04 2.8804779E-02 at 120iterations finished qdiffx linear iterations at : 07:19:58 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 8.1403705E-04 2.8804779E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 07:19:59 7.794u 0.253s 0:08.64 93.0% 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 Tue Oct 11 2011 at 07:19:59 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3169 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.683957 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): 0.1320000 48.45000 ymin,ymax (A): -8.090000 48.85500 zmin,zma (A): 0.9669999 60.65500 x,y,z range (A): 48.31800 56.94500 59.68800 scale (grids/A): 2.683957 object centre (A): 24.29100 20.38250 30.81100 number of atom coordinates read : 3169 total number of charged atoms : 3018 net assigned charge : -1.099989 assigned positive charge : 473.7659 centred at (gu) : 87.76397 87.12466 94.80239 assigned negative charge : -474.8670 centred at (gu) : 87.26109 86.76508 94.46387 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 188278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24638 grid for indexing accessible points = 1.400000 m= 96620 mr = 141610 m= 32171 mr = 80707 m= 6293 mr = 26293 m= 685 mr = 4653 m= 28 mr = 468 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 4506 time to turn everything in is 1.410000 number of dielectric boundary points 70339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 24139 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) : 1.789304 object centre at (A) : 24.29100 20.38250 30.81100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5742394 -9.6040115E-02 midg,1,midg; midg,igrid,midg -0.4058214 8.8177733E-02 1,midg,midg; igrid,midg,midg -0.1698700 0.1310995 gauss-seidel spectral radius is 0.9992286 estimated iterations to convergence 284 setup time was (sec) 1.730000 now iterating at: 07:20:01 rms-change max change #iterations 10.07420 281.0715 at 10iterations 5.800693 119.2183 at 20iterations 3.330614 66.37533 at 30iterations 1.900625 35.20002 at 40iterations 1.082424 21.61667 at 50iterations 0.6185198 10.91850 at 60iterations 0.3521462 6.144593 at 70iterations 0.2004230 3.268858 at 80iterations 0.1141190 2.245358 at 90iterations 6.4933494E-02 1.100555 at 100iterations 3.7001997E-02 0.6770802 at 110iterations 2.1069808E-02 0.3793907 at 120iterations 1.2025329E-02 0.2132645 at 130iterations 6.9048484E-03 0.1336174 at 140iterations 3.9993403E-03 7.0728302E-02 at 150iterations 2.3532617E-03 4.2417526E-02 at 160iterations 1.4178383E-03 2.8964996E-02 at 170iterations 8.8766631E-04 1.6723633E-02 at 180iterations finished qdiffx linear iterations at : 07:20:12 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 8.8766631E-04 1.6723633E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 07:20:12 12.775u 0.258s 0:13.37 97.3% 0+0k 0+0io 0pf+0w