Tue Oct 11 06:07:36 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 06:07:37 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 = 2016 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: 0.7492529 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): 1.829000 40.92600 ymin,ymax (A): -26.27700 17.66200 zmin,zma (A): 38.09500 85.60900 x,y,z range (A): 39.09700 43.93900 47.51400 scale (grids/A): 0.7492529 object centre (A): 21.37750 -4.307500 61.85200 number of atom coordinates read : 2016 total number of charged atoms : 1888 net assigned charge : 6.500006 assigned positive charge : 304.5301 centred at (gu) : 88.27835 90.10143 91.16486 assigned negative charge : -298.0302 centred at (gu) : 88.23186 90.29211 91.23232 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7744 nv = 96 ne = 84 npr = 41103 no. pairs analyzed = 41103 no. exposed pairs = 2432 no. arc points = 16586 no. surface atoms = 833 nbur = 1183 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 583 mr = 4516 m= 6 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1503 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8197 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7632810E-07 7.8312759E-08 midg,1,midg; midg,igrid,midg 3.4757679E-07 -8.0397797E-08 1,midg,midg; igrid,midg,midg 1.1938745E-07 1.4256020E-07 gauss-seidel spectral radius is 0.9906984 estimated iterations to convergence 84 setup time was (sec) 0.5200000 now iterating at: 06:07:37 rms-change max change #iterations 0.2434552 32.18656 at 10iterations 3.4249444E-02 4.380131 at 20iterations 4.7466713E-03 0.7226257 at 30iterations 6.9713750E-04 9.3078613E-02 at 40iterations 1.2271470E-04 1.4141083E-02 at 50iterations finished qdiffx linear iterations at : 06:07:40 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.2271470E-04 1.4141083E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 06:07:40 3.503u 0.164s 0:03.98 91.9% 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 06:07:41 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 = 2016 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: 2.247759 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): 1.829000 40.92600 ymin,ymax (A): -26.27700 17.66200 zmin,zma (A): 38.09500 85.60900 x,y,z range (A): 39.09700 43.93900 47.51400 scale (grids/A): 2.247759 object centre (A): 21.37750 -4.307500 61.85200 number of atom coordinates read : 2016 total number of charged atoms : 1888 net assigned charge : 6.500006 assigned positive charge : 304.5301 centred at (gu) : 84.83504 90.30455 93.49477 assigned negative charge : -298.0302 centred at (gu) : 84.69561 90.87631 93.69701 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16586 grid for indexing accessible points = 1.400000 m= 34472 mr = 58053 m= 7390 mr = 26599 m= 859 mr = 5172 m= 30 mr = 501 m= 0 mr = 3 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 33639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15039 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) : 0.7492529 object centre at (A) : 21.37750 -4.307500 61.85200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6094129E-02 1.6845945E-02 midg,1,midg; midg,igrid,midg 8.1991144E-02 7.5127045E-03 1,midg,midg; igrid,midg,midg 3.9244525E-02 1.1996492E-02 gauss-seidel spectral radius is 0.9989307 estimated iterations to convergence 242 setup time was (sec) 0.9600000 now iterating at: 06:07:42 rms-change max change #iterations 4.965641 177.9622 at 10iterations 2.540536 82.50812 at 20iterations 1.304592 37.78078 at 30iterations 0.6715251 21.38674 at 40iterations 0.3434943 11.13488 at 50iterations 0.1763548 4.717854 at 60iterations 9.0322629E-02 2.580193 at 70iterations 4.6253815E-02 1.244197 at 80iterations 2.3707986E-02 0.7160873 at 90iterations 1.2200579E-02 0.3577566 at 100iterations 6.2859324E-03 0.1802444 at 110iterations 3.2446568E-03 8.9513779E-02 at 120iterations finished qdiffx linear iterations at : 06:07:49 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 3.2446568E-03 8.9513779E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 06:07:49 8.155u 0.217s 0:08.90 93.9% 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 06:07:49 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 = 2016 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: 3.371638 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): 1.829000 40.92600 ymin,ymax (A): -26.27700 17.66200 zmin,zma (A): 38.09500 85.60900 x,y,z range (A): 39.09700 43.93900 47.51400 scale (grids/A): 3.371638 object centre (A): 21.37750 -4.307500 61.85200 number of atom coordinates read : 2016 total number of charged atoms : 1888 net assigned charge : 6.500006 assigned positive charge : 304.5301 centred at (gu) : 82.25271 90.45684 95.24223 assigned negative charge : -298.0302 centred at (gu) : 82.04351 91.31451 95.54554 start vw surface at 0.1400000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 187061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16586 grid for indexing accessible points = 1.400000 m= 104834 mr = 139292 m= 45800 mr = 88238 m= 14398 mr = 38345 m= 3303 mr = 11410 m= 533 mr = 2517 m= 36 mr = 383 m= 0 mr = 13 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.080000 number of dielectric boundary points 75767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 15104 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) : 2.247759 object centre at (A) : 21.37750 -4.307500 61.85200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3876579 9.6102789E-02 midg,1,midg; midg,igrid,midg 0.5865842 4.3134663E-02 1,midg,midg; igrid,midg,midg 0.4197045 5.9244912E-02 gauss-seidel spectral radius is 0.9993214 estimated iterations to convergence 303 setup time was (sec) 2.400000 now iterating at: 06:07:52 rms-change max change #iterations 10.78841 345.7107 at 10iterations 6.450627 178.4719 at 20iterations 3.839540 78.40887 at 30iterations 2.286746 44.94283 at 40iterations 1.357870 22.89411 at 50iterations 0.8038359 15.81254 at 60iterations 0.4755979 7.777808 at 70iterations 0.2817204 4.825232 at 80iterations 0.1666747 2.934181 at 90iterations 9.8587468E-02 1.601288 at 100iterations 5.8232963E-02 0.9225284 at 110iterations 3.4515850E-02 0.5842133 at 120iterations 2.0503983E-02 0.3468933 at 130iterations 1.2237314E-02 0.2087064 at 140iterations 7.3962663E-03 0.1116284 at 150iterations 4.5684767E-03 8.2027435E-02 at 160iterations 2.9030375E-03 5.1521301E-02 at 170iterations 1.9323983E-03 3.4870148E-02 at 180iterations finished qdiffx linear iterations at : 06:08:03 total time elapsed so far: 13.70000 # loops : 180 mean,max change (kT/e) : 1.9323983E-03 3.4870148E-02 energy calculations done at 13.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.89000 DelPhi exited at 06:08:04 13.892u 0.218s 0:14.62 96.4% 0+0k 0+0io 0pf+0w