Mon Oct 10 19:37:01 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+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 Mon Oct 10 2011 at 19:37:01 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 !!! WARNING: HIR 106 has a net charge of 0.5140 !!! WARNING: HIR 232 has a net charge of 0.5140 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: 0.6135815 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): -12.48400 39.82700 ymin,ymax (A): -35.22600 22.79400 zmin,zma (A): 3.810000 61.44900 x,y,z range (A): 52.31100 58.02000 57.63900 scale (grids/A): 0.6135815 object centre (A): 13.67150 -6.216001 32.62950 number of atom coordinates read : 2700 total number of charged atoms : 2564 net assigned charge : 9.528037 assigned positive charge : 403.3456 centred at (gu) : 90.17341 93.13884 89.03819 assigned negative charge : -393.8187 centred at (gu) : 90.20914 93.19694 89.06583 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6850 nv = 96 ne = 84 npr = 52739 no. pairs analyzed = 52739 no. exposed pairs = 3810 no. arc points = 26882 no. surface atoms = 1275 nbur = 1425 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 410 mr = 3387 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2663 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8389 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6671435E-09 3.9109480E-09 midg,1,midg; midg,igrid,midg 4.8400408E-09 5.8994813E-09 1,midg,midg; igrid,midg,midg 7.9716944E-09 4.4979012E-09 gauss-seidel spectral radius is 0.9862676 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 19:37:02 rms-change max change #iterations 0.1196131 17.61500 at 10iterations 1.0979963E-02 1.737167 at 20iterations 1.0374599E-03 0.1496601 at 30iterations 1.2003704E-04 2.0347595E-02 at 40iterations 2.0223733E-05 3.7374496E-03 at 50iterations finished qdiffx linear iterations at : 19:37:05 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.0223733E-05 3.7374496E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 19:37:06 3.428u 0.170s 0:04.19 85.6% 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 19:37:06 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 !!! WARNING: HIR 106 has a net charge of 0.5140 !!! WARNING: HIR 232 has a net charge of 0.5140 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: 1.840744 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): -12.48400 39.82700 ymin,ymax (A): -35.22600 22.79400 zmin,zma (A): 3.810000 61.44900 x,y,z range (A): 52.31100 58.02000 57.63900 scale (grids/A): 1.840744 object centre (A): 13.67150 -6.216001 32.62950 number of atom coordinates read : 2700 total number of charged atoms : 2564 net assigned charge : 9.528037 assigned positive charge : 403.3456 centred at (gu) : 90.51965 99.41592 87.11376 assigned negative charge : -393.8187 centred at (gu) : 90.62740 99.59071 87.19762 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 73418 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26882 grid for indexing accessible points = 1.400000 m= 25637 mr = 47512 m= 4392 mr = 17963 m= 287 mr = 2640 m= 5 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 196 time to turn everything in is 0.3800000 number of dielectric boundary points 35534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 20063 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) : 0.6135815 object centre at (A) : 13.67150 -6.216001 32.62950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7769147E-03 1.3732440E-02 midg,1,midg; midg,igrid,midg 3.2671742E-02 5.3436164E-02 1,midg,midg; igrid,midg,midg 1.6673503E-02 2.5708757E-02 gauss-seidel spectral radius is 0.9985631 estimated iterations to convergence 209 setup time was (sec) 0.6000000 now iterating at: 19:37:06 rms-change max change #iterations 4.027404 166.5498 at 10iterations 1.850301 70.15598 at 20iterations 0.8494700 25.35092 at 30iterations 0.3888730 13.05745 at 40iterations 0.1783240 5.841391 at 50iterations 8.1937253E-02 2.555367 at 60iterations 3.7566617E-02 1.209328 at 70iterations 1.7287534E-02 0.5909615 at 80iterations 7.9357587E-03 0.2713680 at 90iterations 3.6579021E-03 0.1190834 at 100iterations 1.6786368E-03 5.4746628E-02 at 110iterations 7.8056112E-04 2.6883841E-02 at 120iterations finished qdiffx linear iterations at : 19:37:14 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 7.8056112E-04 2.6883841E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 19:37:14 7.913u 0.198s 0:08.63 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 Mon Oct 10 2011 at 19:37:14 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 !!! WARNING: HIR 106 has a net charge of 0.5140 !!! WARNING: HIR 232 has a net charge of 0.5140 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: 2.761117 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): -12.48400 39.82700 ymin,ymax (A): -35.22600 22.79400 zmin,zma (A): 3.810000 61.44900 x,y,z range (A): 52.31100 58.02000 57.63900 scale (grids/A): 2.761117 object centre (A): 13.67150 -6.216001 32.62950 number of atom coordinates read : 2700 total number of charged atoms : 2564 net assigned charge : 9.528037 assigned positive charge : 403.3456 centred at (gu) : 90.77914 104.1235 85.67050 assigned negative charge : -393.8187 centred at (gu) : 90.94098 104.3861 85.79629 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 169558 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26882 grid for indexing accessible points = 1.400000 m= 81892 mr = 116557 m= 30658 mr = 64207 m= 7786 mr = 23833 m= 1146 mr = 5727 m= 76 mr = 729 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 685 time to turn everything in is 0.9500000 number of dielectric boundary points 80050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 20502 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) : 1.840744 object centre at (A) : 13.67150 -6.216001 32.62950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3713412E-03 0.1652671 midg,1,midg; midg,igrid,midg 0.3567955 0.9045119 1,midg,midg; igrid,midg,midg 0.1391253 0.3769987 gauss-seidel spectral radius is 0.9992568 estimated iterations to convergence 290 setup time was (sec) 1.200000 now iterating at: 19:37:16 rms-change max change #iterations 9.912809 338.5890 at 10iterations 5.878078 140.8262 at 20iterations 3.459461 71.24400 at 30iterations 2.017798 40.96804 at 40iterations 1.170513 22.72288 at 50iterations 0.6798772 13.20147 at 60iterations 0.3937595 8.535931 at 70iterations 0.2273075 4.552998 at 80iterations 0.1311261 2.672242 at 90iterations 7.5549155E-02 1.415270 at 100iterations 4.3435968E-02 0.8230247 at 110iterations 2.5003698E-02 0.4923172 at 120iterations 1.4390050E-02 0.2836027 at 130iterations 8.2774684E-03 0.1553116 at 140iterations 4.7776271E-03 0.1063423 at 150iterations 2.7507073E-03 4.8166275E-02 at 160iterations 1.5991705E-03 3.0191422E-02 at 170iterations 9.3140727E-04 1.8570930E-02 at 180iterations finished qdiffx linear iterations at : 19:37:27 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 9.3140727E-04 1.8570930E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 19:37:28 12.879u 0.214s 0:13.53 96.6% 0+0k 0+0io 0pf+0w