Sun Oct 9 14:08:36 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 Sun Oct 9 2011 at 14:08:36 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 = 2432 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: 0.6708374 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): -8.543000 37.18500 ymin,ymax (A): 1.464000 52.27700 zmin,zma (A): -5.235000 47.83300 x,y,z range (A): 45.72800 50.81300 53.06800 scale (grids/A): 0.6708374 object centre (A): 14.32100 26.87050 21.29900 number of atom coordinates read : 2432 total number of charged atoms : 2309 net assigned charge : 5.500015 assigned positive charge : 365.3478 centred at (gu) : 88.73977 90.91198 89.70432 assigned negative charge : -359.8487 centred at (gu) : 88.83099 90.98883 89.76396 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7548 nv = 96 ne = 84 npr = 48376 no. pairs analyzed = 48376 no. exposed pairs = 3181 no. arc points = 22198 no. surface atoms = 1057 nbur = 1375 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 4089 m= 2 mr = 26 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 0.3000000 number of dielectric boundary points 3886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2089 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8648 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4752027E-08 3.8485659E-09 midg,1,midg; midg,igrid,midg 3.0610263E-08 -4.5406393E-10 1,midg,midg; igrid,midg,midg 5.2084985E-08 -2.6241527E-09 gauss-seidel spectral radius is 0.9884706 estimated iterations to convergence 76 setup time was (sec) 0.5100000 now iterating at: 14:08:37 rms-change max change #iterations 0.1714754 31.70152 at 10iterations 1.8326433E-02 2.507027 at 20iterations 2.0461052E-03 0.2729568 at 30iterations 2.2461296E-04 2.9957294E-02 at 40iterations 2.5840385E-05 3.7040710E-03 at 50iterations finished qdiffx linear iterations at : 14:08:39 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 2.5840385E-05 3.7040710E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 14:08:40 3.278u 0.132s 0:03.71 91.6% 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 Sun Oct 9 2011 at 14:08:40 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 = 2432 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: 2.012512 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): -8.543000 37.18500 ymin,ymax (A): 1.464000 52.27700 zmin,zma (A): -5.235000 47.83300 x,y,z range (A): 45.72800 50.81300 53.06800 scale (grids/A): 2.012512 object centre (A): 14.32100 26.87050 21.29900 number of atom coordinates read : 2432 total number of charged atoms : 2309 net assigned charge : 5.500015 assigned positive charge : 365.3478 centred at (gu) : 86.21891 92.73536 89.11234 assigned negative charge : -359.8487 centred at (gu) : 86.49267 92.96646 89.29177 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22198 grid for indexing accessible points = 1.400000 m= 30434 mr = 55088 m= 5138 mr = 22085 m= 342 mr = 3126 m= 7 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 35797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 18264 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) : 0.6708374 object centre at (A) : 14.32100 26.87050 21.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7012179E-02 1.7206637E-02 midg,1,midg; midg,igrid,midg 5.8460407E-02 2.9421370E-02 1,midg,midg; igrid,midg,midg 5.9324838E-03 -3.9873142E-02 gauss-seidel spectral radius is 0.9987656 estimated iterations to convergence 225 setup time was (sec) 0.8400000 now iterating at: 14:08:41 rms-change max change #iterations 4.491373 219.9918 at 10iterations 2.180336 75.67223 at 20iterations 1.056829 36.07804 at 30iterations 0.5147934 15.49484 at 40iterations 0.2501293 7.996902 at 50iterations 0.1211744 3.635056 at 60iterations 5.8914702E-02 1.779236 at 70iterations 2.8719906E-02 0.8409033 at 80iterations 1.3924653E-02 0.4361420 at 90iterations 6.7668548E-03 0.2082300 at 100iterations 3.2859778E-03 0.1093864 at 110iterations 1.5988912E-03 5.5831909E-02 at 120iterations finished qdiffx linear iterations at : 14:08:47 total time elapsed so far: 6.990000 # loops : 120 mean,max change (kT/e) : 1.5988912E-03 5.5831909E-02 energy calculations done at 6.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.180000 DelPhi exited at 14:08:48 7.180u 0.159s 0:07.70 95.1% 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 Sun Oct 9 2011 at 14:08:48 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 = 2432 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.018768 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): -8.543000 37.18500 ymin,ymax (A): 1.464000 52.27700 zmin,zma (A): -5.235000 47.83300 x,y,z range (A): 45.72800 50.81300 53.06800 scale (grids/A): 3.018768 object centre (A): 14.32100 26.87050 21.29900 number of atom coordinates read : 2432 total number of charged atoms : 2309 net assigned charge : 5.500015 assigned positive charge : 365.3478 centred at (gu) : 84.32825 94.10294 88.66840 assigned negative charge : -359.8487 centred at (gu) : 84.73896 94.44955 88.93756 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 184998 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22198 grid for indexing accessible points = 1.400000 m= 96194 mr = 133407 m= 36778 mr = 77871 m= 9344 mr = 29213 m= 1450 mr = 6843 m= 138 mr = 929 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.410000 number of dielectric boundary points 80576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 18467 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) : 2.012512 object centre at (A) : 14.32100 26.87050 21.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9439203 6.8934597E-02 midg,1,midg; midg,igrid,midg 0.6997627 0.2130690 1,midg,midg; igrid,midg,midg 3.5231460E-02 -0.3752165 gauss-seidel spectral radius is 0.9992930 estimated iterations to convergence 297 setup time was (sec) 1.700000 now iterating at: 14:08:49 rms-change max change #iterations 10.51041 444.2194 at 10iterations 6.299376 134.3899 at 20iterations 3.745885 79.64184 at 30iterations 2.218895 50.56845 at 40iterations 1.311410 25.68874 at 50iterations 0.7718793 14.14707 at 60iterations 0.4539743 7.797630 at 70iterations 0.2661515 4.734879 at 80iterations 0.1559405 2.541122 at 90iterations 9.1247201E-02 1.445704 at 100iterations 5.3319030E-02 0.9133713 at 110iterations 3.1137684E-02 0.5567703 at 120iterations 1.8201577E-02 0.3686752 at 130iterations 1.0626713E-02 0.1816487 at 140iterations 6.2017306E-03 0.1163864 at 150iterations 3.6207135E-03 6.1264038E-02 at 160iterations 2.1264614E-03 4.0115356E-02 at 170iterations 1.2475805E-03 2.3139954E-02 at 180iterations finished qdiffx linear iterations at : 14:08:59 total time elapsed so far: 11.08000 # loops : 180 mean,max change (kT/e) : 1.2475805E-03 2.3139954E-02 energy calculations done at 11.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.26000 DelPhi exited at 14:08:59 11.261u 0.166s 0:11.73 97.3% 0+0k 0+0io 0pf+0w