Sat Oct 8 18:48:35 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 Sat Oct 8 2011 at 18:48:35 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! 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: 0.6330014 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): -32.12900 17.55500 ymin,ymax (A): -22.81300 23.94100 zmin,zma (A): -12.15800 44.08200 x,y,z range (A): 49.68400 46.75400 56.24000 scale (grids/A): 0.6330014 object centre (A): -7.286999 0.5640001 15.96200 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.53587 88.66274 89.96723 assigned negative charge : -387.4045 centred at (gu) : 88.44257 88.70847 89.84261 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6863 nv = 96 ne = 84 npr = 54555 no. pairs analyzed = 54555 no. exposed pairs = 3015 no. arc points = 21529 no. surface atoms = 1030 nbur = 1564 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 3855 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2900000 number of dielectric boundary points 3331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2152 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8364 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.3029400E-09 1.6468343E-08 midg,1,midg; midg,igrid,midg 1.2259767E-08 3.8246076E-10 1,midg,midg; igrid,midg,midg -5.9062208E-09 9.9815134E-09 gauss-seidel spectral radius is 0.9870663 estimated iterations to convergence 72 setup time was (sec) 0.5700000 now iterating at: 18:48:36 rms-change max change #iterations 0.1389801 19.03651 at 10iterations 1.3599141E-02 1.974024 at 20iterations 1.3466900E-03 0.2211609 at 30iterations 1.4487637E-04 1.9063950E-02 at 40iterations 1.7378081E-05 2.8972626E-03 at 50iterations finished qdiffx linear iterations at : 18:48:39 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.7378081E-05 2.8972626E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 18:48:40 4.184u 0.224s 0:04.67 94.2% 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 8 2011 at 18:48:40 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! 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: 1.899004 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): -32.12900 17.55500 ymin,ymax (A): -22.81300 23.94100 zmin,zma (A): -12.15800 44.08200 x,y,z range (A): 49.68400 46.75400 56.24000 scale (grids/A): 1.899004 object centre (A): -7.286999 0.5640001 15.96200 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.60712 85.98769 89.90124 assigned negative charge : -387.4045 centred at (gu) : 85.32754 86.12521 89.52777 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 73610 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21529 grid for indexing accessible points = 1.400000 m= 26766 mr = 51766 m= 3987 mr = 19783 m= 233 mr = 2523 m= 4 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 0.6100000 number of dielectric boundary points 30453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19310 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) : 0.6330014 object centre at (A) : -7.286999 0.5640001 15.96200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0482432E-02 2.7455200E-02 midg,1,midg; midg,igrid,midg 1.4080998E-02 2.5724710E-03 1,midg,midg; igrid,midg,midg -2.9518262E-03 3.4122683E-02 gauss-seidel spectral radius is 0.9986207 estimated iterations to convergence 213 setup time was (sec) 0.9400000 now iterating at: 18:48:41 rms-change max change #iterations 4.218151 195.6024 at 10iterations 1.964436 67.56122 at 20iterations 0.9195803 28.76925 at 30iterations 0.4280000 15.76120 at 40iterations 0.2000356 6.930735 at 50iterations 9.3750395E-02 3.327119 at 60iterations 4.3702900E-02 1.332648 at 70iterations 2.0354806E-02 0.7408180 at 80iterations 9.5250877E-03 0.3118172 at 90iterations 4.4544726E-03 0.1562538 at 100iterations 2.0819062E-03 7.6873779E-02 at 110iterations 9.7226311E-04 3.0560493E-02 at 120iterations finished qdiffx linear iterations at : 18:48:49 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 9.7226311E-04 3.0560493E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 18:48:50 9.554u 0.245s 0:10.11 96.8% 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 Sat Oct 8 2011 at 18:48:50 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! 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: 2.848506 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): -32.12900 17.55500 ymin,ymax (A): -22.81300 23.94100 zmin,zma (A): -12.15800 44.08200 x,y,z range (A): 49.68400 46.75400 56.24000 scale (grids/A): 2.848506 object centre (A): -7.286999 0.5640001 15.96200 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 83.41062 83.98144 89.85170 assigned negative charge : -387.4045 centred at (gu) : 82.99123 84.18779 89.29167 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 170001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21529 grid for indexing accessible points = 1.400000 m= 86635 mr = 124562 m= 30821 mr = 71545 m= 7264 mr = 24751 m= 1124 mr = 5495 m= 74 mr = 789 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 656 time to turn everything in is 1.510000 number of dielectric boundary points 68750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 19631 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) : 1.899004 object centre at (A) : -7.286999 0.5640001 15.96200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1612992 0.2731198 midg,1,midg; midg,igrid,midg 0.1714924 3.9363750E-03 1,midg,midg; igrid,midg,midg 1.2481298E-02 0.3935827 gauss-seidel spectral radius is 0.9992484 estimated iterations to convergence 288 setup time was (sec) 1.850000 now iterating at: 18:48:52 rms-change max change #iterations 9.797741 369.7994 at 10iterations 5.669641 148.1480 at 20iterations 3.272265 78.87744 at 30iterations 1.877925 47.59507 at 40iterations 1.079282 20.34101 at 50iterations 0.6190059 12.38570 at 60iterations 0.3553030 6.994810 at 70iterations 0.2037024 3.579020 at 80iterations 0.1167045 2.324996 at 90iterations 6.6866241E-02 1.213663 at 100iterations 3.8324524E-02 0.7685909 at 110iterations 2.1901233E-02 0.3875198 at 120iterations 1.2564177E-02 0.2488966 at 130iterations 7.2236382E-03 0.1303635 at 140iterations 4.1632373E-03 7.9490662E-02 at 150iterations 2.4060130E-03 4.7281265E-02 at 160iterations 1.3999047E-03 2.8827667E-02 at 170iterations 8.2247437E-04 1.6759872E-02 at 180iterations finished qdiffx linear iterations at : 18:49:05 total time elapsed so far: 15.18000 # loops : 180 mean,max change (kT/e) : 8.2247437E-04 1.6759872E-02 energy calculations done at 15.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.36000 DelPhi exited at 18:49:06 15.357u 0.273s 0:15.89 98.3% 0+0k 0+0io 0pf+0w