Tue Oct 11 08:23:00 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 Tue Oct 11 2011 at 08:23:00 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.5990341 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): -10.90200 36.75600 ymin,ymax (A): -27.16400 21.77000 zmin,zma (A): -13.55100 45.87800 x,y,z range (A): 47.65800 48.93400 59.42900 scale (grids/A): 0.5990341 object centre (A): 12.92700 -2.697000 16.16350 number of atom coordinates read : 2756 total number of charged atoms : 2618 net assigned charge : 0.1620197 assigned positive charge : 417.2677 centred at (gu) : 89.86152 90.32355 92.34471 assigned negative charge : -417.1063 centred at (gu) : 89.63335 90.20672 92.18118 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6684 nv = 96 ne = 84 npr = 53785 no. pairs analyzed = 53785 no. exposed pairs = 3437 no. arc points = 24324 no. surface atoms = 1159 nbur = 1597 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 326 mr = 3697 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.4000000 number of dielectric boundary points 3287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2493 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8310 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7368797E-09 1.0392477E-08 midg,1,midg; midg,igrid,midg -4.2328083E-09 4.6170436E-09 1,midg,midg; igrid,midg,midg -9.2404351E-09 8.0704030E-09 gauss-seidel spectral radius is 0.9855927 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 08:23:01 rms-change max change #iterations 0.1117711 18.52168 at 10iterations 9.5878588E-03 1.567164 at 20iterations 9.0632646E-04 0.1400785 at 30iterations 1.1869072E-04 1.8226624E-02 at 40iterations 2.6807944E-05 3.6621094E-03 at 50iterations finished qdiffx linear iterations at : 08:23:04 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 2.6807944E-05 3.6621094E-03 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 08:23:05 4.062u 0.149s 0:04.51 93.1% 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 Tue Oct 11 2011 at 08:23:05 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.797102 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): -10.90200 36.75600 ymin,ymax (A): -27.16400 21.77000 zmin,zma (A): -13.55100 45.87800 x,y,z range (A): 47.65800 48.93400 59.42900 scale (grids/A): 1.797102 object centre (A): 12.92700 -2.697000 16.16350 number of atom coordinates read : 2756 total number of charged atoms : 2618 net assigned charge : 0.1620197 assigned positive charge : 417.2677 centred at (gu) : 89.58401 90.97038 97.03371 assigned negative charge : -417.1063 centred at (gu) : 88.89971 90.61983 96.54326 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24324 grid for indexing accessible points = 1.400000 m= 26425 mr = 50368 m= 3601 mr = 19631 m= 145 mr = 2174 m= 0 mr = 44 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 747 time to turn everything in is 0.6500000 number of dielectric boundary points 30527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 202 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20471 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) : 0.5990341 object centre at (A) : 12.92700 -2.697000 16.16350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2067639E-02 7.4218528E-04 midg,1,midg; midg,igrid,midg -8.7519782E-03 6.2881755E-03 1,midg,midg; igrid,midg,midg -8.1156399E-03 3.1328879E-02 gauss-seidel spectral radius is 0.9984928 estimated iterations to convergence 204 setup time was (sec) 1.010000 now iterating at: 08:23:06 rms-change max change #iterations 3.942568 192.0661 at 10iterations 1.771529 65.97806 at 20iterations 0.8011914 27.29537 at 30iterations 0.3612607 12.44929 at 40iterations 0.1636694 5.695496 at 50iterations 7.3395200E-02 2.493820 at 60iterations 3.3234704E-02 1.102733 at 70iterations 1.5084063E-02 0.5469642 at 80iterations 6.7618480E-03 0.2147560 at 90iterations 3.0748886E-03 9.9177837E-02 at 100iterations 1.3910646E-03 4.2175293E-02 at 110iterations 6.3141505E-04 2.1532059E-02 at 120iterations finished qdiffx linear iterations at : 08:23:15 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 6.3141505E-04 2.1532059E-02 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 08:23:15 9.534u 0.283s 0:10.35 94.7% 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 Tue Oct 11 2011 at 08:23:15 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.695654 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): -10.90200 36.75600 ymin,ymax (A): -27.16400 21.77000 zmin,zma (A): -13.55100 45.87800 x,y,z range (A): 47.65800 48.93400 59.42900 scale (grids/A): 2.695654 object centre (A): 12.92700 -2.697000 16.16350 number of atom coordinates read : 2756 total number of charged atoms : 2618 net assigned charge : 0.1620197 assigned positive charge : 417.2677 centred at (gu) : 89.37587 91.45540 100.5505 assigned negative charge : -417.1063 centred at (gu) : 88.34965 90.92974 99.81487 start vw surface at 0.1900000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 167598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24324 grid for indexing accessible points = 1.400000 m= 86368 mr = 122018 m= 29750 mr = 71016 m= 6267 mr = 23926 m= 735 mr = 4657 m= 21 mr = 438 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 2376 time to turn everything in is 1.670000 number of dielectric boundary points 68684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 20938 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) : 1.797102 object centre at (A) : 12.92700 -2.697000 16.16350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.386254 0.1000994 midg,1,midg; midg,igrid,midg -0.1161316 3.2018207E-02 1,midg,midg; igrid,midg,midg -5.4691955E-02 0.2978124 gauss-seidel spectral radius is 0.9992213 estimated iterations to convergence 283 setup time was (sec) 2.060000 now iterating at: 08:23:18 rms-change max change #iterations 9.481116 289.7603 at 10iterations 5.447119 155.5607 at 20iterations 3.121284 67.86739 at 30iterations 1.783275 37.22200 at 40iterations 1.016703 19.09942 at 50iterations 0.5799208 10.97577 at 60iterations 0.3293720 6.309317 at 70iterations 0.1875815 3.892751 at 80iterations 0.1067418 2.138390 at 90iterations 6.0493056E-02 1.270037 at 100iterations 3.4407370E-02 0.6363659 at 110iterations 1.9517062E-02 0.3649940 at 120iterations 1.1103120E-02 0.2188148 at 130iterations 6.3258763E-03 0.1146736 at 140iterations 3.6059998E-03 6.5433502E-02 at 150iterations 2.0622290E-03 3.9079666E-02 at 160iterations 1.1828456E-03 2.2665024E-02 at 170iterations 6.8733783E-04 1.3382196E-02 at 180iterations finished qdiffx linear iterations at : 08:23:31 total time elapsed so far: 15.31000 # loops : 180 mean,max change (kT/e) : 6.8733783E-04 1.3382196E-02 energy calculations done at 15.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.54000 DelPhi exited at 08:23:32 15.540u 0.291s 0:16.26 97.3% 0+0k 0+0io 0pf+0w