Sat Oct 15 15:32:23 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 Sat Oct 15 2011 at 15:32:23 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 = 2704 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: 0.6623009 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): -11.17800 36.97100 ymin,ymax (A): -25.55500 22.69200 zmin,zma (A): -8.352000 45.40000 x,y,z range (A): 48.14900 48.24700 53.75200 scale (grids/A): 0.6623009 object centre (A): 12.89650 -1.431500 18.52400 number of atom coordinates read : 2704 total number of charged atoms : 2557 net assigned charge : 3.500012 assigned positive charge : 409.3378 centred at (gu) : 90.01913 90.19247 91.16656 assigned negative charge : -405.8383 centred at (gu) : 89.72306 90.00431 91.08582 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7927 nv = 96 ne = 84 npr = 55932 no. pairs analyzed = 55932 no. exposed pairs = 3290 no. arc points = 22784 no. surface atoms = 1098 nbur = 1606 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 4510 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.4100000 number of dielectric boundary points 3806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2211 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9373 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6066939E-09 3.4241172E-08 midg,1,midg; midg,igrid,midg -3.1476777E-08 5.1770201E-08 1,midg,midg; igrid,midg,midg -5.7478488E-08 7.2492078E-08 gauss-seidel spectral radius is 0.9881892 estimated iterations to convergence 75 setup time was (sec) 0.7200000 now iterating at: 15:32:24 rms-change max change #iterations 0.1724226 22.44560 at 10iterations 1.8537756E-02 2.308179 at 20iterations 2.0418270E-03 0.2762852 at 30iterations 2.2389082E-04 2.8530121E-02 at 40iterations 2.6640486E-05 3.9730072E-03 at 50iterations finished qdiffx linear iterations at : 15:32:28 total time elapsed so far: 4.770000 # loops : 50 mean,max change (kT/e) : 2.6640486E-05 3.9730072E-03 energy calculations done at 4.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.990000 DelPhi exited at 15:32:29 4.994u 0.438s 0:05.75 94.2% 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 Sat Oct 15 2011 at 15:32:29 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 = 2704 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: 1.986903 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): -11.17800 36.97100 ymin,ymax (A): -25.55500 22.69200 zmin,zma (A): -8.352000 45.40000 x,y,z range (A): 48.14900 48.24700 53.75200 scale (grids/A): 1.986903 object centre (A): 12.89650 -1.431500 18.52400 number of atom coordinates read : 2704 total number of charged atoms : 2557 net assigned charge : 3.500012 assigned positive charge : 409.3378 centred at (gu) : 90.05670 90.57690 93.49937 assigned negative charge : -405.8383 centred at (gu) : 89.16884 90.01267 93.25735 start vw surface at 0.1600000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 85236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22784 grid for indexing accessible points = 1.400000 m= 31859 mr = 60668 m= 5202 mr = 23600 m= 355 mr = 3265 m= 9 mr = 141 m= 0 mr = 2 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1189 time to turn everything in is 0.8900000 number of dielectric boundary points 34985 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 20183 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) : 0.6623009 object centre at (A) : 12.89650 -1.431500 18.52400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6019080E-02 1.4377293E-02 midg,1,midg; midg,igrid,midg -1.8605014E-02 3.1169306E-02 1,midg,midg; igrid,midg,midg -1.6454583E-02 7.7287249E-02 gauss-seidel spectral radius is 0.9987516 estimated iterations to convergence 224 setup time was (sec) 1.240000 now iterating at: 15:32:30 rms-change max change #iterations 4.744644 289.4428 at 10iterations 2.306005 73.67960 at 20iterations 1.114107 34.13375 at 30iterations 0.5399486 17.96330 at 40iterations 0.2621635 7.417583 at 50iterations 0.1269321 3.913795 at 60iterations 6.1554607E-02 1.839530 at 70iterations 2.9952066E-02 0.9535027 at 80iterations 1.4561756E-02 0.4619598 at 90iterations 7.0550875E-03 0.2010880 at 100iterations 3.4323321E-03 0.1109695 at 110iterations 1.6759438E-03 5.1984787E-02 at 120iterations finished qdiffx linear iterations at : 15:32:41 total time elapsed so far: 11.81000 # loops : 120 mean,max change (kT/e) : 1.6759438E-03 5.1984787E-02 energy calculations done at 11.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.02000 DelPhi exited at 15:32:42 12.029u 0.501s 0:12.93 96.8% 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 Sat Oct 15 2011 at 15:32:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2704 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: 2.980354 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): -11.17800 36.97100 ymin,ymax (A): -25.55500 22.69200 zmin,zma (A): -8.352000 45.40000 x,y,z range (A): 48.14900 48.24700 53.75200 scale (grids/A): 2.980354 object centre (A): 12.89650 -1.431500 18.52400 number of atom coordinates read : 2704 total number of charged atoms : 2557 net assigned charge : 3.500012 assigned positive charge : 409.3378 centred at (gu) : 90.08482 90.86534 95.24892 assigned negative charge : -405.8383 centred at (gu) : 88.75323 90.01901 94.88599 start vw surface at 0.1500000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 196779 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22784 grid for indexing accessible points = 1.400000 m= 102271 mr = 145881 m= 37948 mr = 84527 m= 9458 mr = 30690 m= 1457 mr = 7027 m= 109 mr = 963 m= 3 mr = 64 m= 0 mr = 2 time to grow re-entrant surface = 1.420000 no. cavity mid-points inaccessible to solvent = 3712 time to turn everything in is 2.340000 number of dielectric boundary points 78871 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.500000 number of grid points assigned charge 20456 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) : 1.986903 object centre at (A) : 12.89650 -1.431500 18.52400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3267838 0.3613564 midg,1,midg; midg,igrid,midg -0.1939107 0.3699863 1,midg,midg; igrid,midg,midg -7.5854748E-02 0.6414747 gauss-seidel spectral radius is 0.9992845 estimated iterations to convergence 295 setup time was (sec) 2.730000 now iterating at: 15:32:45 rms-change max change #iterations 10.81239 390.1177 at 10iterations 6.349174 148.6122 at 20iterations 3.722253 65.96355 at 30iterations 2.175981 40.33144 at 40iterations 1.272802 28.81426 at 50iterations 0.7429390 13.35411 at 60iterations 0.4325933 7.637731 at 70iterations 0.2526636 3.978700 at 80iterations 0.1471328 2.615568 at 90iterations 8.5468009E-02 1.437637 at 100iterations 4.9799435E-02 0.9752111 at 110iterations 2.8993076E-02 0.4699783 at 120iterations 1.6900705E-02 0.2977962 at 130iterations 9.8258760E-03 0.1721668 at 140iterations 5.7559987E-03 9.3395233E-02 at 150iterations 3.3807491E-03 5.7010651E-02 at 160iterations 1.9965232E-03 3.4666061E-02 at 170iterations 1.1987366E-03 2.1292210E-02 at 180iterations finished qdiffx linear iterations at : 15:33:03 total time elapsed so far: 21.11000 # loops : 180 mean,max change (kT/e) : 1.1987366E-03 2.1292210E-02 energy calculations done at 21.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.32000 DelPhi exited at 15:33:04 21.329u 0.543s 0:22.48 97.2% 0+0k 0+0io 0pf+0w