Sun Oct 9 13:40:27 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 Sun Oct 9 2011 at 13:40:27 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6952310 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): -0.2040000 45.88700 ymin,ymax (A): 35.64300 85.92400 zmin,zma (A): -24.13400 27.07200 x,y,z range (A): 46.09100 50.28101 51.20600 scale (grids/A): 0.6952310 object centre (A): 22.84150 60.78350 1.469001 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500019 assigned positive charge : 360.6473 centred at (gu) : 89.74173 89.91207 90.79214 assigned negative charge : -359.1476 centred at (gu) : 89.83571 90.12860 90.72883 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7754 nv = 96 ne = 84 npr = 47325 no. pairs analyzed = 47325 no. exposed pairs = 3015 no. arc points = 21066 no. surface atoms = 1011 nbur = 1348 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4293 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1934 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8680 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5576946E-08 4.2513744E-08 midg,1,midg; midg,igrid,midg 1.0231273E-07 -8.4835172E-08 1,midg,midg; igrid,midg,midg 5.1905371E-08 -3.0159164E-08 gauss-seidel spectral radius is 0.9892514 estimated iterations to convergence 79 setup time was (sec) 0.6000000 now iterating at: 13:40:28 rms-change max change #iterations 0.2018509 30.69254 at 10iterations 2.4516989E-02 3.508915 at 20iterations 3.6521847E-03 0.5152435 at 30iterations 8.8858797E-04 0.1309319 at 40iterations 2.9436511E-04 4.4254303E-02 at 50iterations finished qdiffx linear iterations at : 13:40:31 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 2.9436511E-04 4.4254303E-02 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 13:40:31 4.042u 0.259s 0:04.57 93.8% 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 13:40:31 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.085693 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): -0.2040000 45.88700 ymin,ymax (A): 35.64300 85.92400 zmin,zma (A): -24.13400 27.07200 x,y,z range (A): 46.09100 50.28101 51.20600 scale (grids/A): 2.085693 object centre (A): 22.84150 60.78350 1.469001 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500019 assigned positive charge : 360.6473 centred at (gu) : 89.22483 89.73612 92.37602 assigned negative charge : -359.1476 centred at (gu) : 89.50693 90.38567 92.18627 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 82790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21066 grid for indexing accessible points = 1.400000 m= 31461 mr = 57642 m= 5345 mr = 23365 m= 461 mr = 3393 m= 11 mr = 223 m= 0 mr = 4 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 35441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 17587 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) : 0.6952310 object centre at (A) : 22.84150 60.78350 1.469001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3097999E-02 2.3311725E-02 midg,1,midg; midg,igrid,midg 9.3853347E-02 -6.3767754E-02 1,midg,midg; igrid,midg,midg 1.4373829E-03 -6.7904699E-03 gauss-seidel spectral radius is 0.9988326 estimated iterations to convergence 232 setup time was (sec) 1.050000 now iterating at: 13:40:33 rms-change max change #iterations 4.888701 216.9330 at 10iterations 2.411754 76.25636 at 20iterations 1.199506 38.85853 at 30iterations 0.5912237 16.67329 at 40iterations 0.2941681 8.357729 at 50iterations 0.1458602 4.651711 at 60iterations 7.2341211E-02 2.183531 at 70iterations 3.6139611E-02 1.098663 at 80iterations 1.8153379E-02 0.5153909 at 90iterations 9.1883317E-03 0.2684517 at 100iterations 4.7058742E-03 0.1455231 at 110iterations 2.5030083E-03 7.6904297E-02 at 120iterations finished qdiffx linear iterations at : 13:40:41 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 2.5030083E-03 7.6904297E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.570000 DelPhi exited at 13:40:42 9.572u 0.286s 0:10.18 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 Sun Oct 9 2011 at 13:40:42 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.128540 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): -0.2040000 45.88700 ymin,ymax (A): 35.64300 85.92400 zmin,zma (A): -24.13400 27.07200 x,y,z range (A): 46.09100 50.28101 51.20600 scale (grids/A): 3.128540 object centre (A): 22.84150 60.78350 1.469001 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500019 assigned positive charge : 360.6473 centred at (gu) : 88.83724 89.60406 93.56391 assigned negative charge : -359.1476 centred at (gu) : 89.26033 90.57830 93.27930 start vw surface at 0.1400000 fill in re-entrant regions at 1.060000 boundary points on vw surface= 190971 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21066 grid for indexing accessible points = 1.400000 m= 100165 mr = 139255 m= 38171 mr = 82313 m= 9712 mr = 30839 m= 1751 mr = 7307 m= 191 mr = 1224 m= 9 mr = 131 m= 0 mr = 4 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.400000 number of dielectric boundary points 79897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.560000 number of grid points assigned charge 17736 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) : 2.085693 object centre at (A) : 22.84150 60.78350 1.469001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5041540 0.3117048 midg,1,midg; midg,igrid,midg 1.500175 -0.7661102 1,midg,midg; igrid,midg,midg -4.0849015E-02 -3.6336038E-02 gauss-seidel spectral radius is 0.9993023 estimated iterations to convergence 299 setup time was (sec) 2.730000 now iterating at: 13:40:45 rms-change max change #iterations 11.04726 457.0637 at 10iterations 6.572775 136.2485 at 20iterations 3.901421 73.39328 at 30iterations 2.315186 41.48636 at 40iterations 1.371954 24.79232 at 50iterations 0.8100463 14.51538 at 60iterations 0.4770262 9.157597 at 70iterations 0.2806110 4.729952 at 80iterations 0.1648248 2.930127 at 90iterations 9.7184204E-02 1.748119 at 100iterations 5.7156175E-02 0.9333496 at 110iterations 3.3847190E-02 0.5970631 at 120iterations 2.0115627E-02 0.3644142 at 130iterations 1.2147559E-02 0.2234344 at 140iterations 7.5240904E-03 0.1437836 at 150iterations 4.8718988E-03 0.1056862 at 160iterations 3.3235394E-03 7.5416565E-02 at 170iterations 2.4135688E-03 5.1502228E-02 at 180iterations finished qdiffx linear iterations at : 13:40:59 total time elapsed so far: 16.60000 # loops : 180 mean,max change (kT/e) : 2.4135688E-03 5.1502228E-02 energy calculations done at 16.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.77000 DelPhi exited at 13:40:59 16.774u 0.315s 0:17.38 98.2% 0+0k 0+0io 0pf+0w