Tue Oct 11 08:19:47 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+sph.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 = amb.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 08:19:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 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: 0.6943361 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): -16.07300 28.98500 ymin,ymax (A): -13.04700 35.04100 zmin,zma (A): 1.364000 52.63600 x,y,z range (A): 45.05800 48.08800 51.27200 scale (grids/A): 0.6943361 object centre (A): 6.456000 10.99700 27.00000 number of atom coordinates read : 2120 total number of charged atoms : 2003 net assigned charge : 1.000009 assigned positive charge : 314.2545 centred at (gu) : 90.86204 90.32164 89.53802 assigned negative charge : -313.2549 centred at (gu) : 90.90653 90.30698 89.27223 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7060 nv = 96 ne = 84 npr = 43396 no. pairs analyzed = 43396 no. exposed pairs = 2792 no. arc points = 19612 no. surface atoms = 943 nbur = 1177 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 3843 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1720 ## 139 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7916 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0290520E-07 9.3134545E-08 midg,1,midg; midg,igrid,midg 1.4628279E-09 1.3146642E-08 1,midg,midg; igrid,midg,midg 1.9591367E-08 -1.1418930E-08 gauss-seidel spectral radius is 0.9892048 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 08:19:48 rms-change max change #iterations 0.1873000 27.28061 at 10iterations 2.1608861E-02 2.933273 at 20iterations 2.6170260E-03 0.3562279 at 30iterations 3.6015146E-04 5.2146912E-02 at 40iterations 7.3583404E-05 1.2900352E-02 at 50iterations finished qdiffx linear iterations at : 08:19:50 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 7.3583404E-05 1.2900352E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 08:19:51 3.410u 0.166s 0:03.95 90.3% 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 08:19:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 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: 2.083008 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): -16.07300 28.98500 ymin,ymax (A): -13.04700 35.04100 zmin,zma (A): 1.364000 52.63600 x,y,z range (A): 45.05800 48.08800 51.27200 scale (grids/A): 2.083008 object centre (A): 6.456000 10.99700 27.00000 number of atom coordinates read : 2120 total number of charged atoms : 2003 net assigned charge : 1.000009 assigned positive charge : 314.2545 centred at (gu) : 92.58574 90.96460 88.61396 assigned negative charge : -313.2549 centred at (gu) : 92.71957 90.92086 87.81648 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75357 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19612 grid for indexing accessible points = 1.400000 m= 27873 mr = 51810 m= 5191 mr = 20398 m= 404 mr = 3309 m= 18 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3900000 number of dielectric boundary points 33183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 15875 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) : 0.6943361 object centre at (A) : 6.456000 10.99700 27.00000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1351476E-02 7.1583509E-02 midg,1,midg; midg,igrid,midg -2.3493733E-02 -3.7505951E-02 1,midg,midg; igrid,midg,midg 1.2756564E-02 -1.3071804E-02 gauss-seidel spectral radius is 0.9988099 estimated iterations to convergence 229 setup time was (sec) 0.6000000 now iterating at: 08:19:52 rms-change max change #iterations 4.512074 227.1140 at 10iterations 2.210671 72.08569 at 20iterations 1.091265 41.90680 at 30iterations 0.5396069 19.14303 at 40iterations 0.2661969 8.635525 at 50iterations 0.1311789 4.196442 at 60iterations 6.4566590E-02 2.100964 at 70iterations 3.1912763E-02 0.9789391 at 80iterations 1.5708638E-02 0.4922485 at 90iterations 7.7509922E-03 0.2416077 at 100iterations 3.8426258E-03 0.1186028 at 110iterations 1.8947239E-03 6.5466166E-02 at 120iterations finished qdiffx linear iterations at : 08:19:59 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 1.8947239E-03 6.5466166E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 08:20:00 7.947u 0.199s 0:08.68 93.6% 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 Tue Oct 11 2011 at 08:20:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 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: 3.124512 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): -16.07300 28.98500 ymin,ymax (A): -13.04700 35.04100 zmin,zma (A): 1.364000 52.63600 x,y,z range (A): 45.05800 48.08800 51.27200 scale (grids/A): 3.124512 object centre (A): 6.456000 10.99700 27.00000 number of atom coordinates read : 2120 total number of charged atoms : 2003 net assigned charge : 1.000009 assigned positive charge : 314.2545 centred at (gu) : 93.87849 91.44692 87.92074 assigned negative charge : -313.2549 centred at (gu) : 94.07932 91.38120 86.72466 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 174023 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19612 grid for indexing accessible points = 1.400000 m= 87947 mr = 125330 m= 34441 mr = 71620 m= 9536 mr = 27800 m= 1697 mr = 7116 m= 131 mr = 1097 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 1.150000 number of dielectric boundary points 74772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 16016 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) : 2.083008 object centre at (A) : 6.456000 10.99700 27.00000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7739443 0.6792415 midg,1,midg; midg,igrid,midg -0.2127389 -0.4015573 1,midg,midg; igrid,midg,midg 9.3902156E-02 -0.1324654 gauss-seidel spectral radius is 0.9993067 estimated iterations to convergence 300 setup time was (sec) 1.390000 now iterating at: 08:20:01 rms-change max change #iterations 10.15028 441.8464 at 10iterations 5.977684 130.4200 at 20iterations 3.538130 70.68441 at 30iterations 2.084001 42.90981 at 40iterations 1.225855 21.82839 at 50iterations 0.7184200 13.21420 at 60iterations 0.4223603 8.561423 at 70iterations 0.2482874 4.442651 at 80iterations 0.1450086 2.475838 at 90iterations 8.5009664E-02 1.424976 at 100iterations 4.9777213E-02 0.8227425 at 110iterations 2.9095698E-02 0.5314960 at 120iterations 1.7025916E-02 0.3247981 at 130iterations 9.9769151E-03 0.1747746 at 140iterations 5.8364952E-03 0.1073895 at 150iterations 3.4155340E-03 6.0932159E-02 at 160iterations 1.9997957E-03 3.5352230E-02 at 170iterations 1.1747346E-03 2.0469666E-02 at 180iterations finished qdiffx linear iterations at : 08:20:13 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 1.1747346E-03 2.0469666E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 08:20:13 12.949u 0.200s 0:13.53 97.1% 0+0k 0+0io 0pf+0w