Tue Oct 11 02:21:01 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 Tue Oct 11 2011 at 02:21:01 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: FMN 398 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6677420 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): 20.70800 67.24900 ymin,ymax (A): 14.65700 67.97100 zmin,zma (A): -17.36500 29.85700 x,y,z range (A): 46.54100 53.31400 47.22200 scale (grids/A): 0.6677420 object centre (A): 43.97850 41.31400 6.246000 number of atom coordinates read : 2680 total number of charged atoms : 2545 net assigned charge : 2.500011 assigned positive charge : 408.8235 centred at (gu) : 90.85991 90.33403 90.34605 assigned negative charge : -406.3244 centred at (gu) : 90.69237 90.54635 90.39133 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8065 nv = 96 ne = 84 npr = 54972 no. pairs analyzed = 54972 no. exposed pairs = 3282 no. arc points = 22491 no. surface atoms = 1104 nbur = 1576 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 442 mr = 4608 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.2100000 number of dielectric boundary points 3847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2164 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9431 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7796340E-08 -4.0204227E-09 midg,1,midg; midg,igrid,midg 5.6032164E-08 -5.0407341E-08 1,midg,midg; igrid,midg,midg -2.9337757E-08 5.8932912E-08 gauss-seidel spectral radius is 0.9883811 estimated iterations to convergence 76 setup time was (sec) 0.4100000 now iterating at: 02:21:02 rms-change max change #iterations 0.1833462 29.46634 at 10iterations 2.0770475E-02 3.150942 at 20iterations 3.0406846E-03 0.4989586 at 30iterations 8.0808299E-04 0.1720009 at 40iterations 2.8394081E-04 6.2057495E-02 at 50iterations finished qdiffx linear iterations at : 02:21:05 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.8394081E-04 6.2057495E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 02:21:06 3.448u 0.171s 0:04.29 84.1% 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 Tue Oct 11 2011 at 02:21:06 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: FMN 398 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.003226 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): 20.70800 67.24900 ymin,ymax (A): 14.65700 67.97100 zmin,zma (A): -17.36500 29.85700 x,y,z range (A): 46.54100 53.31400 47.22200 scale (grids/A): 2.003226 object centre (A): 43.97850 41.31400 6.246000 number of atom coordinates read : 2680 total number of charged atoms : 2545 net assigned charge : 2.500011 assigned positive charge : 408.8235 centred at (gu) : 92.57921 91.00117 91.03729 assigned negative charge : -406.3244 centred at (gu) : 92.07698 91.63872 91.17348 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 87195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22491 grid for indexing accessible points = 1.400000 m= 32745 mr = 62013 m= 5546 mr = 24761 m= 373 mr = 3606 m= 6 mr = 172 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1555 time to turn everything in is 0.4500000 number of dielectric boundary points 35313 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 20135 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) : 0.6677420 object centre at (A) : 43.97850 41.31400 6.246000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4660481E-02 -3.4234826E-02 midg,1,midg; midg,igrid,midg 6.0423821E-02 -5.3516198E-02 1,midg,midg; igrid,midg,midg -2.3067823E-02 5.1631354E-02 gauss-seidel spectral radius is 0.9987696 estimated iterations to convergence 226 setup time was (sec) 0.6700000 now iterating at: 02:21:07 rms-change max change #iterations 4.835899 191.1859 at 10iterations 2.352674 84.44600 at 20iterations 1.146641 35.01810 at 30iterations 0.5593612 16.75299 at 40iterations 0.2721873 8.164126 at 50iterations 0.1327389 3.981500 at 60iterations 6.4981841E-02 1.981167 at 70iterations 3.1742673E-02 0.9366679 at 80iterations 1.5746800E-02 0.4710159 at 90iterations 7.9361731E-03 0.2575455 at 100iterations 4.1353730E-03 0.1370697 at 110iterations 2.2761459E-03 8.3545685E-02 at 120iterations finished qdiffx linear iterations at : 02:21:14 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 2.2761459E-03 8.3545685E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 02:21:16 8.040u 0.185s 0:09.96 82.5% 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 Tue Oct 11 2011 at 02:21:16 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: FMN 398 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.004839 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): 20.70800 67.24900 ymin,ymax (A): 14.65700 67.97100 zmin,zma (A): -17.36500 29.85700 x,y,z range (A): 46.54100 53.31400 47.22200 scale (grids/A): 3.004839 object centre (A): 43.97850 41.31400 6.246000 number of atom coordinates read : 2680 total number of charged atoms : 2545 net assigned charge : 2.500011 assigned positive charge : 408.8235 centred at (gu) : 93.86861 91.50153 91.55583 assigned negative charge : -406.3244 centred at (gu) : 93.11552 92.45807 91.76019 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 201431 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22491 grid for indexing accessible points = 1.400000 m= 104925 mr = 149893 m= 39769 mr = 87049 m= 10239 mr = 32533 m= 1695 mr = 7853 m= 123 mr = 1224 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 5161 time to turn everything in is 1.120000 number of dielectric boundary points 79567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 20359 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) : 2.003226 object centre at (A) : 43.97850 41.31400 6.246000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1740216 -0.3914554 midg,1,midg; midg,igrid,midg 0.8449249 -0.6754454 1,midg,midg; igrid,midg,midg -0.2466595 0.4130681 gauss-seidel spectral radius is 0.9992923 estimated iterations to convergence 297 setup time was (sec) 1.360000 now iterating at: 02:21:17 rms-change max change #iterations 11.04799 469.1649 at 10iterations 6.520051 132.3746 at 20iterations 3.844773 75.76643 at 30iterations 2.257249 39.42089 at 40iterations 1.326036 23.56028 at 50iterations 0.7748119 13.59041 at 60iterations 0.4536871 7.931065 at 70iterations 0.2654448 5.779369 at 80iterations 0.1550610 3.142883 at 90iterations 9.0409748E-02 1.501251 at 100iterations 5.2916899E-02 0.8540001 at 110iterations 3.0908953E-02 0.5146484 at 120iterations 1.8199988E-02 0.3087730 at 130iterations 1.0745345E-02 0.2071228 at 140iterations 6.4664036E-03 0.1377106 at 150iterations 3.9753718E-03 8.5136414E-02 at 160iterations 2.5663849E-03 5.6533813E-02 at 170iterations 1.7518275E-03 4.1297913E-02 at 180iterations finished qdiffx linear iterations at : 02:21:29 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 1.7518275E-03 4.1297913E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 02:21:30 13.023u 0.215s 0:13.90 95.1% 0+0k 0+0io 0pf+0w