Tue Oct 11 08:34:20 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 Tue Oct 11 2011 at 08:34:20 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2086 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.7012291 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): -19.56200 26.14400 ymin,ymax (A): -12.58200 28.37800 zmin,zma (A): -2.379000 48.38900 x,y,z range (A): 45.70600 40.96000 50.76800 scale (grids/A): 0.7012291 object centre (A): 3.290999 7.898000 23.00500 number of atom coordinates read : 2086 total number of charged atoms : 1965 net assigned charge : 5.564011 assigned positive charge : 320.6260 centred at (gu) : 89.24496 89.85877 90.04313 assigned negative charge : -315.0621 centred at (gu) : 89.13416 89.89077 90.09097 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6848 nv = 96 ne = 84 npr = 41528 no. pairs analyzed = 41528 no. exposed pairs = 2584 no. arc points = 17293 no. surface atoms = 876 nbur = 1210 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 3911 m= 7 mr = 89 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 0.2800000 number of dielectric boundary points 3315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1581 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7751 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1062629E-08 2.0190996E-08 midg,1,midg; midg,igrid,midg 5.6260390E-08 2.6281709E-08 1,midg,midg; igrid,midg,midg -9.4344896E-09 7.6359200E-08 gauss-seidel spectral radius is 0.9893992 estimated iterations to convergence 79 setup time was (sec) 0.5300000 now iterating at: 08:34:21 rms-change max change #iterations 0.1989414 30.35651 at 10iterations 2.5170652E-02 3.863373 at 20iterations 3.7060478E-03 0.4991130 at 30iterations 7.8449206E-04 0.1029320 at 40iterations 2.3515726E-04 2.8625488E-02 at 50iterations finished qdiffx linear iterations at : 08:34:23 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.3515726E-04 2.8625488E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 08:34:24 3.445u 0.174s 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 08:34:24 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2086 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.103687 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): -19.56200 26.14400 ymin,ymax (A): -12.58200 28.37800 zmin,zma (A): -2.379000 48.38900 x,y,z range (A): 45.70600 40.96000 50.76800 scale (grids/A): 2.103687 object centre (A): 3.290999 7.898000 23.00500 number of atom coordinates read : 2086 total number of charged atoms : 1965 net assigned charge : 5.564011 assigned positive charge : 320.6260 centred at (gu) : 87.73490 89.57633 90.12941 assigned negative charge : -315.0621 centred at (gu) : 87.40245 89.67230 90.27284 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17293 grid for indexing accessible points = 1.400000 m= 28770 mr = 51792 m= 5566 mr = 21686 m= 478 mr = 3649 m= 11 mr = 227 m= 0 mr = 1 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 30582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15590 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) : 0.7012291 object centre at (A) : 3.290999 7.898000 23.00500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3211906E-02 6.4424828E-02 midg,1,midg; midg,igrid,midg 2.4829499E-02 3.3635597E-03 1,midg,midg; igrid,midg,midg 3.0177720E-03 2.3840234E-02 gauss-seidel spectral radius is 0.9988111 estimated iterations to convergence 230 setup time was (sec) 0.8600000 now iterating at: 08:34:25 rms-change max change #iterations 4.589322 175.4539 at 10iterations 2.264154 76.93080 at 20iterations 1.113149 34.77302 at 30iterations 0.5530194 17.14986 at 40iterations 0.2728630 9.244862 at 50iterations 0.1348006 4.347357 at 60iterations 6.6548653E-02 2.234945 at 70iterations 3.2960702E-02 1.097302 at 80iterations 1.6428092E-02 0.5351372 at 90iterations 8.2811778E-03 0.2671661 at 100iterations 4.1915341E-03 0.1244416 at 110iterations 2.1969073E-03 7.8760147E-02 at 120iterations finished qdiffx linear iterations at : 08:34:32 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 2.1969073E-03 7.8760147E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 08:34:33 7.799u 0.238s 0:08.38 95.7% 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 Tue Oct 11 2011 at 08:34:33 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2086 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 3.155531 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): -19.56200 26.14400 ymin,ymax (A): -12.58200 28.37800 zmin,zma (A): -2.379000 48.38900 x,y,z range (A): 45.70600 40.96000 50.76800 scale (grids/A): 3.155531 object centre (A): 3.290999 7.898000 23.00500 number of atom coordinates read : 2086 total number of charged atoms : 1965 net assigned charge : 5.564011 assigned positive charge : 320.6260 centred at (gu) : 86.60239 89.36448 90.19410 assigned negative charge : -315.0621 centred at (gu) : 86.10358 89.50843 90.40926 start vw surface at 0.1500000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 168611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17293 grid for indexing accessible points = 1.400000 m= 90112 mr = 125069 m= 36349 mr = 74517 m= 10502 mr = 29756 m= 1915 mr = 8043 m= 164 mr = 1280 m= 7 mr = 83 m= 0 mr = 1 time to grow re-entrant surface = 0.8799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.830000 number of dielectric boundary points 68911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 15720 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) : 2.103687 object centre at (A) : 3.290999 7.898000 23.00500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3139999 1.126405 midg,1,midg; midg,igrid,midg 0.2115715 1.0970016E-03 1,midg,midg; igrid,midg,midg 9.7634219E-02 0.1820849 gauss-seidel spectral radius is 0.9992902 estimated iterations to convergence 296 setup time was (sec) 2.140000 now iterating at: 08:34:35 rms-change max change #iterations 10.26849 379.1598 at 10iterations 6.082128 136.9986 at 20iterations 3.587259 66.33042 at 30iterations 2.113860 41.50075 at 40iterations 1.243383 25.72437 at 50iterations 0.7303280 13.16015 at 60iterations 0.4270602 9.040606 at 70iterations 0.2500204 4.784599 at 80iterations 0.1470698 2.489017 at 90iterations 8.5872546E-02 1.989898 at 100iterations 5.0523497E-02 1.004486 at 110iterations 2.9883118E-02 0.4837151 at 120iterations 1.7869685E-02 0.3551941 at 130iterations 1.0939022E-02 0.2013359 at 140iterations 6.9136075E-03 0.1282883 at 150iterations 4.5868922E-03 8.2201004E-02 at 160iterations 3.2390114E-03 5.7643890E-02 at 170iterations 2.4142917E-03 3.9287567E-02 at 180iterations finished qdiffx linear iterations at : 08:34:46 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 2.4142917E-03 3.9287567E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 08:34:46 12.879u 0.231s 0:13.79 94.9% 0+0k 0+0io 0pf+0w