Sat Oct 15 11:26:51 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 15 2011 at 11:26:51 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! 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: ZN4 430 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7008702 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): -5.639000 43.83600 ymin,ymax (A): -2.979000 47.81500 zmin,zma (A): -7.982000 40.35900 x,y,z range (A): 49.47500 50.79400 48.34100 scale (grids/A): 0.7008702 object centre (A): 19.09850 22.41800 16.18850 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 394.9950 centred at (gu) : 88.39040 91.86758 90.58655 assigned negative charge : -390.7956 centred at (gu) : 88.27276 91.97892 90.53071 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8704 nv = 96 ne = 84 npr = 54610 no. pairs analyzed = 54610 no. exposed pairs = 2995 no. arc points = 21584 no. surface atoms = 1006 nbur = 1600 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 597 mr = 5108 m= 3 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 397 time to turn everything in is 0.2000000 number of dielectric boundary points 4063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1959 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9795 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4839724E-09 6.9334398E-08 midg,1,midg; midg,igrid,midg 6.3031905E-08 -4.1014935E-08 1,midg,midg; igrid,midg,midg -4.3502443E-08 6.8618050E-08 gauss-seidel spectral radius is 0.9894418 estimated iterations to convergence 79 setup time was (sec) 0.4500000 now iterating at: 11:26:52 rms-change max change #iterations 0.2189903 31.78565 at 10iterations 2.6746279E-02 3.762905 at 20iterations 3.2074640E-03 0.4273758 at 30iterations 3.9342127E-04 5.2988052E-02 at 40iterations 4.9647544E-05 5.8441162E-03 at 50iterations finished qdiffx linear iterations at : 11:26:55 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 4.9647544E-05 5.8441162E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 11:26:56 4.175u 0.272s 0:04.85 91.5% 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 15 2011 at 11:26:56 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! 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: ZN4 430 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.102611 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): -5.639000 43.83600 ymin,ymax (A): -2.979000 47.81500 zmin,zma (A): -7.982000 40.35900 x,y,z range (A): 49.47500 50.79400 48.34100 scale (grids/A): 2.102611 object centre (A): 19.09850 22.41800 16.18850 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 394.9950 centred at (gu) : 85.17075 95.60210 91.75906 assigned negative charge : -390.7956 centred at (gu) : 84.81814 95.93658 91.59183 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 91777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21584 grid for indexing accessible points = 1.400000 m= 37796 mr = 65320 m= 7821 mr = 29438 m= 727 mr = 5526 m= 19 mr = 437 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 9199 time to turn everything in is 0.4900000 number of dielectric boundary points 37419 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19564 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) : 0.7008702 object centre at (A) : 19.09850 22.41800 16.18850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7787440E-03 2.5171144E-02 midg,1,midg; midg,igrid,midg 2.7604129E-03 -2.8409822E-02 1,midg,midg; igrid,midg,midg -1.1275477E-02 9.0409666E-02 gauss-seidel spectral radius is 0.9988595 estimated iterations to convergence 234 setup time was (sec) 0.7900000 now iterating at: 11:26:57 rms-change max change #iterations 5.178213 214.9524 at 10iterations 2.571982 77.06887 at 20iterations 1.285842 37.80484 at 30iterations 0.6398418 19.42705 at 40iterations 0.3211080 9.420341 at 50iterations 0.1605075 4.254463 at 60iterations 8.0191463E-02 2.326439 at 70iterations 4.0203910E-02 1.175186 at 80iterations 2.0126285E-02 0.5186882 at 90iterations 1.0051798E-02 0.2887497 at 100iterations 5.0307834E-03 0.1440201 at 110iterations 2.5185659E-03 6.7466736E-02 at 120iterations finished qdiffx linear iterations at : 11:27:06 total time elapsed so far: 9.520000 # loops : 120 mean,max change (kT/e) : 2.5185659E-03 6.7466736E-02 energy calculations done at 9.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 11:27:06 9.658u 0.350s 0:10.50 95.2% 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 15 2011 at 11:27:07 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! 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: ZN4 430 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.153916 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): -5.639000 43.83600 ymin,ymax (A): -2.979000 47.81500 zmin,zma (A): -7.982000 40.35900 x,y,z range (A): 49.47500 50.79400 48.34100 scale (grids/A): 3.153916 object centre (A): 19.09850 22.41800 16.18850 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 394.9950 centred at (gu) : 82.75592 98.40324 92.63847 assigned negative charge : -390.7956 centred at (gu) : 82.22712 98.90479 92.38766 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 211427 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21584 grid for indexing accessible points = 1.400000 m= 116326 mr = 156610 m= 49605 mr = 98253 m= 15187 mr = 41805 m= 3126 mr = 12186 m= 397 mr = 2416 m= 11 mr = 268 m= 0 mr = 4 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 30951 time to turn everything in is 1.600000 number of dielectric boundary points 84537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 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) : 2.102611 object centre at (A) : 19.09850 22.41800 16.18850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2158542 0.2109793 midg,1,midg; midg,igrid,midg -5.6147307E-02 -0.2290340 1,midg,midg; igrid,midg,midg -0.1652921 1.318128 gauss-seidel spectral radius is 0.9993109 estimated iterations to convergence 301 setup time was (sec) 2.000000 now iterating at: 11:27:09 rms-change max change #iterations 11.44767 410.4914 at 10iterations 6.759402 141.4418 at 20iterations 3.983078 76.37286 at 30iterations 2.341146 48.29247 at 40iterations 1.380465 26.08702 at 50iterations 0.8120016 12.74932 at 60iterations 0.4778035 7.794331 at 70iterations 0.2803879 4.683942 at 80iterations 0.1642533 2.636518 at 90iterations 9.6425883E-02 1.433132 at 100iterations 5.6622609E-02 0.9013438 at 110iterations 3.3186201E-02 0.5334301 at 120iterations 1.9485192E-02 0.3212013 at 130iterations 1.1427049E-02 0.1762543 at 140iterations 6.7045898E-03 0.1043334 at 150iterations 3.9377152E-03 6.0109615E-02 at 160iterations 2.3102812E-03 3.7482381E-02 at 170iterations 1.3559940E-03 2.2189140E-02 at 180iterations finished qdiffx linear iterations at : 11:27:24 total time elapsed so far: 17.32000 # loops : 180 mean,max change (kT/e) : 1.3559940E-03 2.2189140E-02 energy calculations done at 17.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.44000 DelPhi exited at 11:27:25 17.446u 0.467s 0:18.26 98.0% 0+0k 0+0io 0pf+0w