Mon Oct 10 09:44:07 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 Mon Oct 10 2011 at 09:44:07 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 = 2921 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: 0.5412967 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): -43.58900 22.17900 ymin,ymax (A): 109.6240 165.3030 zmin,zma (A): 155.1940 208.3210 x,y,z range (A): 65.76800 55.67899 53.12700 scale (grids/A): 0.5412967 object centre (A): -10.70500 137.4635 181.7575 number of atom coordinates read : 2921 total number of charged atoms : 2769 net assigned charge : 7.000015 assigned positive charge : 427.6998 centred at (gu) : 88.45467 89.45049 86.89045 assigned negative charge : -420.7003 centred at (gu) : 88.29347 89.36359 86.71877 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5704 nv = 96 ne = 84 npr = 56688 no. pairs analyzed = 56688 no. exposed pairs = 4305 no. arc points = 31443 no. surface atoms = 1435 nbur = 1486 mkacc time = 0.1300000 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 = 1.568000 m= 244 mr = 2473 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3154 ## 415 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7471 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1505406E-09 5.9430949E-10 midg,1,midg; midg,igrid,midg -5.7554631E-11 7.4281664E-10 1,midg,midg; igrid,midg,midg -6.6995254E-10 8.3431817E-10 gauss-seidel spectral radius is 0.9824203 estimated iterations to convergence 62 setup time was (sec) 0.5800000 now iterating at: 09:44:08 rms-change max change #iterations 6.8955459E-02 13.59756 at 10iterations 4.3983259E-03 0.8662810 at 20iterations 2.9578572E-04 5.7748318E-02 at 30iterations 2.4128476E-05 3.5400391E-03 at 40iterations 3.5111336E-06 4.3106079E-04 at 50iterations finished qdiffx linear iterations at : 09:44:11 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 3.5111336E-06 4.3106079E-04 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 09:44:11 3.365u 0.137s 0:03.86 90.4% 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 10 2011 at 09:44:11 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 = 2921 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: 1.623890 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): -43.58900 22.17900 ymin,ymax (A): 109.6240 165.3030 zmin,zma (A): 155.1940 208.3210 x,y,z range (A): 65.76800 55.67899 53.12700 scale (grids/A): 1.623890 object centre (A): -10.70500 137.4635 181.7575 number of atom coordinates read : 2921 total number of charged atoms : 2769 net assigned charge : 7.000015 assigned positive charge : 427.6998 centred at (gu) : 85.36354 88.35100 80.67071 assigned negative charge : -420.7003 centred at (gu) : 84.88027 88.09067 80.15601 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 61812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31443 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18784 mr = 37742 m= 2041 mr = 11887 m= 74 mr = 828 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 32250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 365 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 21206 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) : 0.5412967 object centre at (A) : -10.70500 137.4635 181.7575 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9805862E-03 8.7318867E-03 midg,1,midg; midg,igrid,midg -3.2362915E-03 1.7396221E-02 1,midg,midg; igrid,midg,midg -1.6630411E-02 2.0313790E-02 gauss-seidel spectral radius is 0.9981713 estimated iterations to convergence 186 setup time was (sec) 0.7900000 now iterating at: 09:44:12 rms-change max change #iterations 3.168899 148.2195 at 10iterations 1.307729 55.47586 at 20iterations 0.5397949 19.99168 at 30iterations 0.2229861 8.600184 at 40iterations 9.2162132E-02 3.306633 at 50iterations 3.8129043E-02 1.390282 at 60iterations 1.5833940E-02 0.6534595 at 70iterations 6.5556280E-03 0.2473164 at 80iterations 2.7231397E-03 9.7476244E-02 at 90iterations 1.1263471E-03 4.5855045E-02 at 100iterations 4.6843805E-04 1.8924713E-02 at 110iterations 1.9475738E-04 6.9046021E-03 at 120iterations finished qdiffx linear iterations at : 09:44:19 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.9475738E-04 6.9046021E-03 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 09:44:20 7.835u 0.223s 0:08.35 96.4% 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 10 2011 at 09:44:20 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 = 2921 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: 2.435835 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): -43.58900 22.17900 ymin,ymax (A): 109.6240 165.3030 zmin,zma (A): 155.1940 208.3210 x,y,z range (A): 65.76800 55.67899 53.12700 scale (grids/A): 2.435835 object centre (A): -10.70500 137.4635 181.7575 number of atom coordinates read : 2921 total number of charged atoms : 2769 net assigned charge : 7.000015 assigned positive charge : 427.6998 centred at (gu) : 83.04521 87.52631 76.00589 assigned negative charge : -420.7003 centred at (gu) : 82.32023 87.13584 75.23389 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 142876 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31443 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 63297 mr = 93332 m= 18941 mr = 47198 m= 3030 mr = 13372 m= 200 mr = 1673 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.150000 number of dielectric boundary points 72708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 22127 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) : 1.623890 object centre at (A) : -10.70500 137.4635 181.7575 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4078930E-02 0.1110869 midg,1,midg; midg,igrid,midg -0.1758720 0.3439893 1,midg,midg; igrid,midg,midg -0.5167725 0.6792796 gauss-seidel spectral radius is 0.9991386 estimated iterations to convergence 269 setup time was (sec) 1.460000 now iterating at: 09:44:21 rms-change max change #iterations 8.549534 364.0801 at 10iterations 4.892591 130.1788 at 20iterations 2.753140 83.79379 at 30iterations 1.544594 44.21578 at 40iterations 0.8639738 23.19452 at 50iterations 0.4818706 12.14840 at 60iterations 0.2667983 6.726383 at 70iterations 0.1480137 3.252920 at 80iterations 8.1491493E-02 2.014038 at 90iterations 4.5013633E-02 1.113506 at 100iterations 2.4848264E-02 0.5904446 at 110iterations 1.3700522E-02 0.3076096 at 120iterations 7.5274548E-03 0.1638155 at 130iterations 4.1494612E-03 0.1061668 at 140iterations 2.2809641E-03 5.2917480E-02 at 150iterations 1.2511327E-03 2.6668549E-02 at 160iterations 6.9080514E-04 1.4458179E-02 at 170iterations 3.7891799E-04 8.4514618E-03 at 180iterations finished qdiffx linear iterations at : 09:44:32 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 3.7891799E-04 8.4514618E-03 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 09:44:32 12.272u 0.228s 0:12.76 97.8% 0+0k 0+0io 0pf+0w