Mon Oct 10 17:13:57 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 17:13:57 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: 378 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: HIZ 236 has a net charge of 0.2000 !!! WARNING: HIZ 251 has a net charge of 0.2000 !!! WARNING: HIY 264 has a net charge of 0.2000 !!! WARNING: HIZ 286 has a net charge of 0.2000 !!! WARNING: HIZ 290 has a net charge of 0.2000 !!! WARNING: HIZ 296 has a net charge of 0.2000 !!! WARNING: HIT 315 has a net charge of 0.5140 !!! WARNING: ASP 334 has a net charge of -2.0000 !!! WARNING: ZN3 336 has a net charge of 1.4000 !!! WARNING: ZN3 338 has a net charge of 1.4000 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: 0.6770249 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): 26.80700 79.39000 ymin,ymax (A): 2.741000 47.85800 zmin,zma (A): -6.855000 35.02000 x,y,z range (A): 52.58300 45.11700 41.87500 scale (grids/A): 0.6770249 object centre (A): 53.09850 25.29950 14.08250 number of atom coordinates read : 1954 total number of charged atoms : 1825 net assigned charge : -2.485987 assigned positive charge : 286.3731 centred at (gu) : 86.82784 89.71577 90.65257 assigned negative charge : -288.8592 centred at (gu) : 86.98879 89.77991 90.57538 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6168 nv = 96 ne = 84 npr = 40214 no. pairs analyzed = 40214 no. exposed pairs = 2689 no. arc points = 19491 no. surface atoms = 900 nbur = 1054 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3049 m= 0 mr = 24 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3300000 number of dielectric boundary points 3452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1749 ## 130 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 6943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5012147E-08 6.8174697E-09 midg,1,midg; midg,igrid,midg 3.2259386E-09 -2.4164553E-08 1,midg,midg; igrid,midg,midg 4.7879364E-08 -2.5182125E-08 gauss-seidel spectral radius is 0.9886410 estimated iterations to convergence 77 setup time was (sec) 0.6400000 now iterating at: 17:13:58 rms-change max change #iterations 0.1696382 26.28871 at 10iterations 1.8798431E-02 3.282768 at 20iterations 2.0679811E-03 0.3350368 at 30iterations 2.3145482E-04 3.2632828E-02 at 40iterations 2.6201657E-05 4.4441223E-03 at 50iterations finished qdiffx linear iterations at : 17:14:02 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 2.6201657E-05 4.4441223E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.700000 DelPhi exited at 17:14:03 4.701u 0.402s 0:05.62 90.7% 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 Mon Oct 10 2011 at 17:14:03 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: 378 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: HIZ 236 has a net charge of 0.2000 !!! WARNING: HIZ 251 has a net charge of 0.2000 !!! WARNING: HIY 264 has a net charge of 0.2000 !!! WARNING: HIZ 286 has a net charge of 0.2000 !!! WARNING: HIZ 290 has a net charge of 0.2000 !!! WARNING: HIZ 296 has a net charge of 0.2000 !!! WARNING: HIT 315 has a net charge of 0.5140 !!! WARNING: ASP 334 has a net charge of -2.0000 !!! WARNING: ZN3 336 has a net charge of 1.4000 !!! WARNING: ZN3 338 has a net charge of 1.4000 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: 2.031075 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): 26.80700 79.39000 ymin,ymax (A): 2.741000 47.85800 zmin,zma (A): -6.855000 35.02000 x,y,z range (A): 52.58300 45.11700 41.87500 scale (grids/A): 2.031075 object centre (A): 53.09850 25.29950 14.08250 number of atom coordinates read : 1954 total number of charged atoms : 1825 net assigned charge : -2.485987 assigned positive charge : 286.3731 centred at (gu) : 80.48355 89.14735 91.95779 assigned negative charge : -288.8592 centred at (gu) : 80.96651 89.33972 91.72610 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 65531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19491 grid for indexing accessible points = 1.400000 m= 21956 mr = 42247 m= 3299 mr = 15104 m= 176 mr = 1867 m= 7 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 686 time to turn everything in is 0.6600000 number of dielectric boundary points 31688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 14480 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) : 0.6770249 object centre at (A) : 53.09850 25.29950 14.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5130647E-02 6.0164247E-04 midg,1,midg; midg,igrid,midg 2.7608801E-02 -4.0644702E-02 1,midg,midg; igrid,midg,midg 6.1382007E-02 -4.1562121E-02 gauss-seidel spectral radius is 0.9987457 estimated iterations to convergence 224 setup time was (sec) 0.9800000 now iterating at: 17:14:04 rms-change max change #iterations 4.155188 179.5425 at 10iterations 2.000504 92.89377 at 20iterations 0.9689927 32.26676 at 30iterations 0.4669329 16.19081 at 40iterations 0.2249968 7.320820 at 50iterations 0.1087150 3.761243 at 60iterations 5.2629236E-02 1.818892 at 70iterations 2.5394250E-02 0.9773159 at 80iterations 1.2255451E-02 0.4044304 at 90iterations 5.8842101E-03 0.2054386 at 100iterations 2.8480981E-03 9.5102787E-02 at 110iterations 1.3706059E-03 4.6791077E-02 at 120iterations finished qdiffx linear iterations at : 17:14:14 total time elapsed so far: 10.92000 # loops : 120 mean,max change (kT/e) : 1.3706059E-03 4.6791077E-02 energy calculations done at 10.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.14000 DelPhi exited at 17:14:15 11.143u 0.492s 0:11.99 96.9% 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 17:14:15 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: 378 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: HIZ 236 has a net charge of 0.2000 !!! WARNING: HIZ 251 has a net charge of 0.2000 !!! WARNING: HIY 264 has a net charge of 0.2000 !!! WARNING: HIZ 286 has a net charge of 0.2000 !!! WARNING: HIZ 290 has a net charge of 0.2000 !!! WARNING: HIZ 296 has a net charge of 0.2000 !!! WARNING: HIT 315 has a net charge of 0.5140 !!! WARNING: ASP 334 has a net charge of -2.0000 !!! WARNING: ZN3 336 has a net charge of 1.4000 !!! WARNING: ZN3 338 has a net charge of 1.4000 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: 3.046612 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): 26.80700 79.39000 ymin,ymax (A): 2.741000 47.85800 zmin,zma (A): -6.855000 35.02000 x,y,z range (A): 52.58300 45.11700 41.87500 scale (grids/A): 3.046612 object centre (A): 53.09850 25.29950 14.08250 number of atom coordinates read : 1954 total number of charged atoms : 1825 net assigned charge : -2.485987 assigned positive charge : 286.3731 centred at (gu) : 75.72534 88.72108 92.93667 assigned negative charge : -288.8592 centred at (gu) : 76.44977 89.00958 92.58920 start vw surface at 0.1400000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 151398 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19491 grid for indexing accessible points = 1.400000 m= 71310 mr = 103279 m= 24534 mr = 55888 m= 5661 mr = 18718 m= 759 mr = 4006 m= 69 mr = 498 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 2493 time to turn everything in is 1.780000 number of dielectric boundary points 71307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 14600 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) : 2.031075 object centre at (A) : 53.09850 25.29950 14.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1628097 -6.9445066E-02 midg,1,midg; midg,igrid,midg 0.2760354 -0.5066272 1,midg,midg; igrid,midg,midg 0.9270924 -0.4194908 gauss-seidel spectral radius is 0.9992983 estimated iterations to convergence 298 setup time was (sec) 2.150000 now iterating at: 17:14:17 rms-change max change #iterations 9.607540 477.2293 at 10iterations 5.691887 156.9322 at 20iterations 3.355678 77.83410 at 30iterations 1.981226 46.26777 at 40iterations 1.166246 25.65830 at 50iterations 0.6836495 13.97790 at 60iterations 0.4012673 7.861284 at 70iterations 0.2340254 5.027531 at 80iterations 0.1369478 2.840827 at 90iterations 7.9957269E-02 1.601152 at 100iterations 4.6671372E-02 0.8688259 at 110iterations 2.7264075E-02 0.5050049 at 120iterations 1.5867600E-02 0.2954502 at 130iterations 9.2680063E-03 0.1789150 at 140iterations 5.4084905E-03 0.1054020 at 150iterations 3.1523411E-03 5.6448936E-02 at 160iterations 1.8405556E-03 3.4031868E-02 at 170iterations 1.0728233E-03 2.1091461E-02 at 180iterations finished qdiffx linear iterations at : 17:14:34 total time elapsed so far: 18.40000 # loops : 180 mean,max change (kT/e) : 1.0728233E-03 2.1091461E-02 energy calculations done at 18.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.62000 DelPhi exited at 17:14:35 18.625u 0.490s 0:19.78 96.6% 0+0k 0+0io 0pf+0w