Mon Oct 22 14:15:54 PDT 2007 #!/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 Mon Oct 22 2007 at 14:15:55 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: 17 atomic charges read from file fort.12 # of charge parameter records: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4443 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: 0.3624147 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 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): -60.40600 -7.504000 ymin,ymax (A): -15.98600 82.24400 zmin,zma (A): -14.58800 50.80200 x,y,z range (A): 52.90200 98.23000 65.39000 scale (grids/A): 0.3624147 object centre (A): -33.95500 33.12900 18.10700 number of atom coordinates read : 4443 total number of charged atoms : 4293 net assigned charge : 11.00003 assigned positive charge : 664.9346 centred at (gu) : 91.22662 91.30518 88.60583 assigned negative charge : -653.9381 centred at (gu) : 91.17878 91.07351 88.50434 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 3203 nv = 96 ne = 84 npr = 91621 no. pairs analyzed = 91621 no. exposed pairs = 5883 no. arc points = 40263 no. surface atoms = 1993 nbur = 2450 mkacc time = 0.2600000 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 = 2.324000 m= 68 mr = 1272 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 2000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2870 ## 891 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 4739 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7010573E-12 4.8857476E-12 midg,1,midg; midg,igrid,midg -5.9753838E-12 2.0074541E-11 1,midg,midg; igrid,midg,midg 2.3184026E-13 7.1466483E-12 gauss-seidel spectral radius is 0.9730840 estimated iterations to convergence 51 setup time was (sec) 0.7300000 now iterating at: 14:15:56 rms-change max change #iterations 1.6924078E-02 4.482368 at 10iterations 5.7475030E-04 0.1486359 at 20iterations 1.8320279E-05 4.0283203E-03 at 30iterations 6.1807657E-07 1.9836426E-04 at 40iterations 3.6916621E-08 1.5258789E-05 at 50iterations finished qdiffx linear iterations at : 14:16:00 total time elapsed so far: 4.770000 # loops : 50 mean,max change (kT/e) : 3.6916621E-08 1.5258789E-05 energy calculations done at 4.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.950000 DelPhi exited at 14:16:01 4.956u 0.404s 0:06.12 87.4% 0+0k 0+0io 6pf+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 Mon Oct 22 2007 at 14:16:01 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: 17 atomic charges read from file fort.12 # of charge parameter records: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4443 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: 1.087244 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 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): -60.40600 -7.504000 ymin,ymax (A): -15.98600 82.24400 zmin,zma (A): -14.58800 50.80200 x,y,z range (A): 52.90200 98.23000 65.39000 scale (grids/A): 1.087244 object centre (A): -33.95500 33.12900 18.10700 number of atom coordinates read : 4443 total number of charged atoms : 4293 net assigned charge : 11.00003 assigned positive charge : 664.9346 centred at (gu) : 93.67855 93.91441 85.81629 assigned negative charge : -653.9381 centred at (gu) : 93.53584 93.22038 85.51306 start vw surface at 0.1500000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 38785 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40263 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.184000 m= 5923 mr = 23031 m= 135 mr = 2630 m= 0 mr = 2 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 19180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1070 ## 73 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 26744 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) : 0.3624147 object centre at (A) : -33.95500 33.12900 18.10700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0310926E-03 1.3608969E-03 midg,1,midg; midg,igrid,midg -7.1496163E-03 1.0114611E-02 1,midg,midg; igrid,midg,midg -2.1049107E-04 8.0891163E-04 gauss-seidel spectral radius is 0.9970093 estimated iterations to convergence 146 setup time was (sec) 0.7000000 now iterating at: 14:16:03 rms-change max change #iterations 1.748176 122.0349 at 10iterations 0.5676151 30.25457 at 20iterations 0.1837639 10.69880 at 30iterations 5.9316758E-02 3.986534 at 40iterations 1.9313794E-02 0.9447892 at 50iterations 6.2330333E-03 0.3876529 at 60iterations 2.0412977E-03 0.1330547 at 70iterations 6.6338183E-04 3.3317566E-02 at 80iterations 2.1576138E-04 1.0852814E-02 at 90iterations 7.1876602E-05 4.8637390E-03 at 100iterations 2.4002920E-05 1.4495850E-03 at 110iterations 8.2893685E-06 6.1035156E-04 at 120iterations finished qdiffx linear iterations at : 14:16:12 total time elapsed so far: 9.760000 # loops : 120 mean,max change (kT/e) : 8.2893685E-06 6.1035156E-04 energy calculations done at 9.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.940000 DelPhi exited at 14:16:13 9.944u 0.564s 0:12.30 85.3% 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 Mon Oct 22 2007 at 14:16:14 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: 17 atomic charges read from file fort.12 # of charge parameter records: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4443 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: 1.630866 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 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): -60.40600 -7.504000 ymin,ymax (A): -15.98600 82.24400 zmin,zma (A): -14.58800 50.80200 x,y,z range (A): 52.90200 98.23000 65.39000 scale (grids/A): 1.630866 object centre (A): -33.95500 33.12900 18.10700 number of atom coordinates read : 4443 total number of charged atoms : 4293 net assigned charge : 11.00003 assigned positive charge : 664.9346 centred at (gu) : 95.51755 95.87116 83.72408 assigned negative charge : -653.9381 centred at (gu) : 95.30368 94.83066 83.26955 start vw surface at 0.1700000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 91885 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40263 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.156000 m= 25802 mr = 59218 m= 2479 mr = 16491 m= 62 mr = 1133 m= 0 mr = 4 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 43382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 492 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 32952 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) : 1.087244 object centre at (A) : -33.95500 33.12900 18.10700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5568677E-02 2.5597274E-02 midg,1,midg; midg,igrid,midg -0.1641963 0.3706341 1,midg,midg; igrid,midg,midg -6.0411398E-03 1.7855449E-02 gauss-seidel spectral radius is 0.9986470 estimated iterations to convergence 215 setup time was (sec) 1.280000 now iterating at: 14:16:16 rms-change max change #iterations 5.559170 302.8455 at 10iterations 2.710342 118.6703 at 20iterations 1.300823 46.49473 at 30iterations 0.6196156 20.25272 at 40iterations 0.2940394 10.57085 at 50iterations 0.1394786 4.602710 at 60iterations 6.5808415E-02 2.156523 at 70iterations 3.1104779E-02 0.9513607 at 80iterations 1.4653236E-02 0.5276947 at 90iterations 6.9236849E-03 0.2276025 at 100iterations 3.2576465E-03 9.5569611E-02 at 110iterations 1.5342562E-03 4.7435760E-02 at 120iterations 7.2040397E-04 2.5300980E-02 at 130iterations 3.3867464E-04 1.1964798E-02 at 140iterations 1.5920449E-04 4.8580170E-03 at 150iterations 7.4948854E-05 2.4385452E-03 at 160iterations 3.5340414E-05 9.9182129E-04 at 170iterations 1.6602544E-05 4.7779083E-04 at 180iterations finished qdiffx linear iterations at : 14:16:31 total time elapsed so far: 15.84000 # loops : 180 mean,max change (kT/e) : 1.6602544E-05 4.7779083E-04 energy calculations done at 15.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.01000 DelPhi exited at 14:16:31 16.017u 0.484s 0:17.06 96.6% 0+0k 0+0io 0pf+0w