Mon Oct 10 14:00:16 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 Mon Oct 10 2011 at 14:00:16 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4416 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5482405 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): 16.63800 78.33600 ymin,ymax (A): 118.3840 183.3190 zmin,zma (A): -1.359000 59.79600 x,y,z range (A): 61.69800 64.93500 61.15500 scale (grids/A): 0.5482405 object centre (A): 47.48700 150.8515 29.21850 number of atom coordinates read : 4416 total number of charged atoms : 4249 net assigned charge : 2.500045 assigned positive charge : 681.1031 centred at (gu) : 91.61954 89.55727 87.28429 assigned negative charge : -678.6061 centred at (gu) : 91.58664 89.45728 87.27677 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8516 nv = 96 ne = 84 npr = 88626 no. pairs analyzed = 88626 no. exposed pairs = 5333 no. arc points = 37519 no. surface atoms = 1794 nbur = 2622 mkacc time = 0.2400000 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= 390 mr = 4567 m= 0 mr = 33 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3933 ## 543 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11357 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6465494E-10 1.3134725E-10 midg,1,midg; midg,igrid,midg -1.0438576E-09 1.1153657E-09 1,midg,midg; igrid,midg,midg -1.2493272E-10 7.8857054E-10 gauss-seidel spectral radius is 0.9829514 estimated iterations to convergence 63 setup time was (sec) 0.7800000 now iterating at: 14:00:17 rms-change max change #iterations 9.2960641E-02 15.43802 at 10iterations 6.5243496E-03 0.9876251 at 20iterations 6.2433491E-04 8.3480835E-02 at 30iterations 1.3133096E-04 1.7701149E-02 at 40iterations 3.7045924E-05 5.3739548E-03 at 50iterations finished qdiffx linear iterations at : 14:00:20 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 3.7045924E-05 5.3739548E-03 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 14:00:21 4.390u 0.258s 0:05.26 88.2% 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 14:00:22 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4416 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.644722 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): 16.63800 78.33600 ymin,ymax (A): 118.3840 183.3190 zmin,zma (A): -1.359000 59.79600 x,y,z range (A): 61.69800 64.93500 61.15500 scale (grids/A): 1.644722 object centre (A): 47.48700 150.8515 29.21850 number of atom coordinates read : 4416 total number of charged atoms : 4249 net assigned charge : 2.500045 assigned positive charge : 681.1031 centred at (gu) : 94.85725 88.67100 81.85165 assigned negative charge : -678.6061 centred at (gu) : 94.75961 88.37157 81.82993 start vw surface at 0.2200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 94714 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37519 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 29282 mr = 65700 m= 3384 mr = 20121 m= 94 mr = 1801 m= 0 mr = 16 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 231 time to turn everything in is 0.7800000 number of dielectric boundary points 39836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 444 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 32636 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) : 0.5482405 object centre at (A) : 47.48700 150.8515 29.21850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6036175E-03 9.3201948E-03 midg,1,midg; midg,igrid,midg 1.9757930E-02 3.7272893E-02 1,midg,midg; igrid,midg,midg -1.1706197E-02 -1.5861120E-02 gauss-seidel spectral radius is 0.9983488 estimated iterations to convergence 195 setup time was (sec) 1.110000 now iterating at: 14:00:23 rms-change max change #iterations 4.311453 212.1063 at 10iterations 1.860468 75.97102 at 20iterations 0.8057586 27.77394 at 30iterations 0.3493916 13.34859 at 40iterations 0.1524144 4.688817 at 50iterations 6.6314690E-02 2.026216 at 60iterations 2.8859397E-02 0.9971542 at 70iterations 1.2530796E-02 0.3642368 at 80iterations 5.4797963E-03 0.1696634 at 90iterations 2.3906033E-03 8.3974838E-02 at 100iterations 1.0551128E-03 3.2337189E-02 at 110iterations 4.6749372E-04 1.4015198E-02 at 120iterations finished qdiffx linear iterations at : 14:00:32 total time elapsed so far: 9.980000 # loops : 120 mean,max change (kT/e) : 4.6749372E-04 1.4015198E-02 energy calculations done at 9.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.16000 DelPhi exited at 14:00:33 10.167u 0.261s 0:11.04 94.3% 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 10 2011 at 14:00:33 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4416 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 2.467083 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): 16.63800 78.33600 ymin,ymax (A): 118.3840 183.3190 zmin,zma (A): -1.359000 59.79600 x,y,z range (A): 61.69800 64.93500 61.15500 scale (grids/A): 2.467083 object centre (A): 47.48700 150.8515 29.21850 number of atom coordinates read : 4416 total number of charged atoms : 4249 net assigned charge : 2.500045 assigned positive charge : 681.1031 centred at (gu) : 97.28559 88.00610 77.77731 assigned negative charge : -678.6061 centred at (gu) : 97.13955 87.55730 77.74496 start vw surface at 0.1900000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 220834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37519 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 101374 mr = 160990 m= 29432 mr = 80324 m= 5612 mr = 22182 m= 494 mr = 3959 m= 6 mr = 261 m= 0 mr = 0 time to grow re-entrant surface = 0.9999999 no. cavity mid-points inaccessible to solvent = 708 time to turn everything in is 1.700000 number of dielectric boundary points 90036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 33956 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) : 1.644722 object centre at (A) : 47.48700 150.8515 29.21850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8526412E-02 0.2175854 midg,1,midg; midg,igrid,midg 0.3686560 0.6812094 1,midg,midg; igrid,midg,midg -0.1809873 -0.2510040 gauss-seidel spectral radius is 0.9992151 estimated iterations to convergence 282 setup time was (sec) 2.060000 now iterating at: 14:00:35 rms-change max change #iterations 11.03020 365.7805 at 10iterations 6.369882 140.8488 at 20iterations 3.655751 72.72191 at 30iterations 2.090916 49.68732 at 40iterations 1.195201 26.19967 at 50iterations 0.6788850 12.24786 at 60iterations 0.3864990 8.502443 at 70iterations 0.2191128 4.119236 at 80iterations 0.1241403 2.187898 at 90iterations 7.0350908E-02 1.207458 at 100iterations 3.9709765E-02 0.7133632 at 110iterations 2.2565627E-02 0.4046869 at 120iterations 1.2744117E-02 0.2403870 at 130iterations 7.2146030E-03 0.1273994 at 140iterations 4.0801666E-03 6.9940567E-02 at 150iterations 2.3104821E-03 4.2890072E-02 at 160iterations 1.3039995E-03 2.1674156E-02 at 170iterations 7.4199436E-04 1.2940407E-02 at 180iterations finished qdiffx linear iterations at : 14:00:49 total time elapsed so far: 15.93000 # loops : 180 mean,max change (kT/e) : 7.4199436E-04 1.2940407E-02 energy calculations done at 15.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.11000 DelPhi exited at 14:00:50 16.114u 0.269s 0:17.05 96.0% 0+0k 0+0io 0pf+0w