Sat Oct 8 19:00:59 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 Sat Oct 8 2011 at 19:00:59 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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: 0.6308701 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): -31.86200 17.51200 ymin,ymax (A): -23.78600 23.23900 zmin,zma (A): -12.51500 43.91500 x,y,z range (A): 49.37400 47.02500 56.43000 scale (grids/A): 0.6308701 object centre (A): -7.174999 -0.2734995 15.70000 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 88.54350 89.19485 89.95389 assigned negative charge : -390.0956 centred at (gu) : 88.43753 89.24002 89.84261 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6826 nv = 96 ne = 84 npr = 54746 no. pairs analyzed = 54746 no. exposed pairs = 2973 no. arc points = 21612 no. surface atoms = 998 nbur = 1608 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 3860 m= 4 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 281 time to turn everything in is 0.3000000 number of dielectric boundary points 3242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2167 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8328 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1418287E-09 1.4979955E-08 midg,1,midg; midg,igrid,midg 1.0978674E-08 8.9692503E-10 1,midg,midg; igrid,midg,midg -6.4796319E-09 1.0716776E-08 gauss-seidel spectral radius is 0.9869813 estimated iterations to convergence 72 setup time was (sec) 0.6100000 now iterating at: 19:01:00 rms-change max change #iterations 0.1388602 19.29673 at 10iterations 1.3328912E-02 2.171673 at 20iterations 1.2980222E-03 0.1845016 at 30iterations 1.2222365E-04 1.8882751E-02 at 40iterations 1.2057376E-05 1.7395020E-03 at 50iterations finished qdiffx linear iterations at : 19:01:04 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 1.2057376E-05 1.7395020E-03 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 19:01:05 4.502u 0.397s 0:05.17 94.5% 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 Sat Oct 8 2011 at 19:01:05 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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: 1.892610 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): -31.86200 17.51200 ymin,ymax (A): -23.78600 23.23900 zmin,zma (A): -12.51500 43.91500 x,y,z range (A): 49.37400 47.02500 56.43000 scale (grids/A): 1.892610 object centre (A): -7.174999 -0.2734995 15.70000 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 85.62983 87.58428 89.86139 assigned negative charge : -390.0956 centred at (gu) : 85.31235 87.71978 89.52777 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73847 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21612 grid for indexing accessible points = 1.400000 m= 26326 mr = 51959 m= 3978 mr = 19733 m= 219 mr = 2543 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 8411 time to turn everything in is 0.5900000 number of dielectric boundary points 30069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 19385 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) : 0.6308701 object centre at (A) : -7.174999 -0.2734995 15.70000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7785097E-02 2.8209832E-02 midg,1,midg; midg,igrid,midg 1.6430415E-02 1.9796125E-03 1,midg,midg; igrid,midg,midg -3.7819738E-03 3.8907837E-02 gauss-seidel spectral radius is 0.9986143 estimated iterations to convergence 213 setup time was (sec) 0.9200000 now iterating at: 19:01:06 rms-change max change #iterations 4.144666 167.8608 at 10iterations 1.935155 70.86800 at 20iterations 0.9012325 32.76281 at 30iterations 0.4177561 13.63859 at 40iterations 0.1951379 5.878056 at 50iterations 9.1178760E-02 3.013940 at 60iterations 4.2242993E-02 1.411980 at 70iterations 1.9729666E-02 0.6152124 at 80iterations 9.2191547E-03 0.2980604 at 90iterations 4.2740782E-03 0.1538758 at 100iterations 1.9923490E-03 6.6257477E-02 at 110iterations 9.2986145E-04 3.2389164E-02 at 120iterations finished qdiffx linear iterations at : 19:01:16 total time elapsed so far: 10.57000 # loops : 120 mean,max change (kT/e) : 9.2986145E-04 3.2389164E-02 energy calculations done at 10.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.74000 DelPhi exited at 19:01:16 10.740u 0.462s 0:11.58 96.7% 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 Sat Oct 8 2011 at 19:01:16 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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: 2.838915 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): -31.86200 17.51200 ymin,ymax (A): -23.78600 23.23900 zmin,zma (A): -12.51500 43.91500 x,y,z range (A): 49.37400 47.02500 56.43000 scale (grids/A): 2.838915 object centre (A): -7.174999 -0.2734995 15.70000 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 83.44453 86.37625 89.79204 assigned negative charge : -390.0956 centred at (gu) : 82.96841 86.57956 89.29156 start vw surface at 0.1300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 170752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21612 grid for indexing accessible points = 1.400000 m= 85916 mr = 125261 m= 30358 mr = 71262 m= 7232 mr = 24651 m= 995 mr = 5526 m= 48 mr = 711 m= 0 mr = 16 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 28371 time to turn everything in is 1.540000 number of dielectric boundary points 67874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 19728 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) : 1.892610 object centre at (A) : -7.174999 -0.2734995 15.70000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1053641 0.3329293 midg,1,midg; midg,igrid,midg 0.2090240 1.9602319E-02 1,midg,midg; igrid,midg,midg -1.3197334E-02 0.4464025 gauss-seidel spectral radius is 0.9992446 estimated iterations to convergence 287 setup time was (sec) 1.860000 now iterating at: 19:01:19 rms-change max change #iterations 9.704650 368.8639 at 10iterations 5.590345 107.8346 at 20iterations 3.196493 62.50985 at 30iterations 1.823563 41.03275 at 40iterations 1.044058 21.82822 at 50iterations 0.5963887 11.30989 at 60iterations 0.3410476 5.951215 at 70iterations 0.1944953 3.635469 at 80iterations 0.1111287 2.181938 at 90iterations 6.3462727E-02 1.128441 at 100iterations 3.6237989E-02 0.7623100 at 110iterations 2.0693015E-02 0.4003534 at 120iterations 1.1785506E-02 0.2072744 at 130iterations 6.7420560E-03 0.1197128 at 140iterations 3.8497392E-03 6.6425323E-02 at 150iterations 2.1981504E-03 4.0786743E-02 at 160iterations 1.2538343E-03 2.3488998E-02 at 170iterations 7.1587373E-04 1.2928009E-02 at 180iterations finished qdiffx linear iterations at : 19:01:34 total time elapsed so far: 17.68000 # loops : 180 mean,max change (kT/e) : 7.1587373E-04 1.2928009E-02 energy calculations done at 17.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.85000 DelPhi exited at 19:01:35 17.851u 0.460s 0:18.58 98.5% 0+0k 0+0io 0pf+0w