Mon Oct 10 00:27:22 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 00:27:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5631 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4929314 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): -17.22000 55.00100 ymin,ymax (A): -29.24800 39.19100 zmin,zma (A): 17.00200 81.10400 x,y,z range (A): 72.22100 68.43900 64.10200 scale (grids/A): 0.4929314 object centre (A): 18.89050 4.971501 49.05300 number of atom coordinates read : 5631 total number of charged atoms : 5477 net assigned charge : -18.50000 assigned positive charge : 841.3843 centred at (gu) : 90.15599 89.07437 90.88916 assigned negative charge : -859.8918 centred at (gu) : 89.97405 89.01242 91.01781 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8722 nv = 96 ne = 84 npr = 114074 no. pairs analyzed = 114074 no. exposed pairs = 7143 no. arc points = 48495 no. surface atoms = 2397 nbur = 3234 mkacc time = 0.2700000 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 = 1.736000 m= 310 mr = 4552 m= 0 mr = 12 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 4468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4677 ## 735 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 11721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1521381E-11 -3.8257519E-10 midg,1,midg; midg,igrid,midg -2.6009320E-10 -2.0868229E-11 1,midg,midg; igrid,midg,midg -3.6347966E-10 1.4610807E-10 gauss-seidel spectral radius is 0.9790231 estimated iterations to convergence 57 setup time was (sec) 0.7600000 now iterating at: 00:27:23 rms-change max change #iterations 6.2523179E-02 9.855179 at 10iterations 3.8458398E-03 0.5186944 at 20iterations 6.7097292E-04 9.8932266E-02 at 30iterations 2.2992271E-04 2.9501796E-02 at 40iterations 9.3762719E-05 1.4883399E-02 at 50iterations finished qdiffx linear iterations at : 00:27:25 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 9.3762719E-05 1.4883399E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 00:27:26 3.539u 0.150s 0:04.02 91.5% 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 00:27:26 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 = 5631 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.478794 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): -17.22000 55.00100 ymin,ymax (A): -29.24800 39.19100 zmin,zma (A): 17.00200 81.10400 x,y,z range (A): 72.22100 68.43900 64.10200 scale (grids/A): 1.478794 object centre (A): 18.89050 4.971501 49.05300 number of atom coordinates read : 5631 total number of charged atoms : 5477 net assigned charge : -18.50000 assigned positive charge : 841.3843 centred at (gu) : 90.46600 87.22145 92.66621 assigned negative charge : -859.8918 centred at (gu) : 89.92184 87.03724 93.05351 start vw surface at 0.2300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 99877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48495 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 28236 mr = 69357 m= 2197 mr = 18338 m= 38 mr = 774 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.7300000 number of dielectric boundary points 41880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 634 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 40679 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) : 0.4929314 object centre at (A) : 18.89050 4.971501 49.05300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7102983E-03 -2.6756208E-02 midg,1,midg; midg,igrid,midg -1.7425247E-02 5.5591483E-03 1,midg,midg; igrid,midg,midg -3.1175442E-02 8.5438276E-03 gauss-seidel spectral radius is 0.9980313 estimated iterations to convergence 179 setup time was (sec) 1.020000 now iterating at: 00:27:27 rms-change max change #iterations 3.842742 149.1581 at 10iterations 1.544910 52.25510 at 20iterations 0.6204443 21.04371 at 30iterations 0.2496266 7.695031 at 40iterations 0.1005979 3.236845 at 50iterations 4.0554039E-02 1.340919 at 60iterations 1.6372275E-02 0.5169449 at 70iterations 6.6568791E-03 0.2361259 at 80iterations 2.7293975E-03 8.4234238E-02 at 90iterations 1.1432500E-03 3.8497925E-02 at 100iterations 5.0901796E-04 1.6048431E-02 at 110iterations 2.5794038E-04 8.8005066E-03 at 120iterations finished qdiffx linear iterations at : 00:27:34 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 2.5794038E-04 8.8005066E-03 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.390000 DelPhi exited at 00:27:35 8.388u 0.162s 0:08.83 96.7% 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 00:27:35 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 = 5631 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.218191 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): -17.22000 55.00100 ymin,ymax (A): -29.24800 39.19100 zmin,zma (A): 17.00200 81.10400 x,y,z range (A): 72.22100 68.43900 64.10200 scale (grids/A): 2.218191 object centre (A): 18.89050 4.971501 49.05300 number of atom coordinates read : 5631 total number of charged atoms : 5477 net assigned charge : -18.50000 assigned positive charge : 841.3843 centred at (gu) : 90.69870 85.83170 93.99865 assigned negative charge : -859.8918 centred at (gu) : 89.88264 85.55565 94.58026 start vw surface at 0.2300000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 233288 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48495 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 102618 mr = 170960 m= 24494 mr = 79334 m= 2851 mr = 16928 m= 109 mr = 1584 m= 0 mr = 13 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 165 time to turn everything in is 1.760000 number of dielectric boundary points 94541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 43651 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) : 1.478794 object centre at (A) : 18.89050 4.971501 49.05300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5340603E-02 -0.4860980 midg,1,midg; midg,igrid,midg -0.3185099 7.9760291E-02 1,midg,midg; igrid,midg,midg -0.5460868 4.8142828E-02 gauss-seidel spectral radius is 0.9991570 estimated iterations to convergence 272 setup time was (sec) 2.070000 now iterating at: 00:27:37 rms-change max change #iterations 10.82181 300.5150 at 10iterations 6.225050 146.6347 at 20iterations 3.557975 84.22127 at 30iterations 2.013393 45.95250 at 40iterations 1.137076 30.38681 at 50iterations 0.6388887 12.80707 at 60iterations 0.3583737 7.069193 at 70iterations 0.2002165 4.076576 at 80iterations 0.1116161 2.106740 at 90iterations 6.2099334E-02 1.135132 at 100iterations 3.4669049E-02 0.6574026 at 110iterations 1.9286655E-02 0.3363647 at 120iterations 1.0716782E-02 0.1930618 at 130iterations 5.9533631E-03 0.1041365 at 140iterations 3.3150658E-03 6.0611725E-02 at 150iterations 1.8448774E-03 3.1711578E-02 at 160iterations 1.0352022E-03 2.1087646E-02 at 170iterations 5.8576459E-04 1.0299683E-02 at 180iterations finished qdiffx linear iterations at : 00:27:48 total time elapsed so far: 13.00000 # loops : 180 mean,max change (kT/e) : 5.8576459E-04 1.0299683E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 00:27:48 13.193u 0.168s 0:13.63 97.9% 0+0k 0+0io 0pf+0w