Mon Oct 10 14:00:13 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 Mon Oct 10 2011 at 14:00:13 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 = 3101 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: 0.5548196 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): -9.530000 48.15900 ymin,ymax (A): -19.25300 29.61100 zmin,zma (A): -22.72800 41.43700 x,y,z range (A): 57.68900 48.86400 64.16500 scale (grids/A): 0.5548196 object centre (A): 19.31450 5.179000 9.354500 number of atom coordinates read : 3101 total number of charged atoms : 2966 net assigned charge : 3.500005 assigned positive charge : 471.9679 centred at (gu) : 88.31868 89.11704 90.63683 assigned negative charge : -468.4690 centred at (gu) : 88.23973 89.11200 90.51021 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6344 nv = 96 ne = 84 npr = 61842 no. pairs analyzed = 61842 no. exposed pairs = 4140 no. arc points = 28833 no. surface atoms = 1373 nbur = 1728 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 268 mr = 3224 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3381 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2952 ## 368 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8157 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.9159579E-10 1.7727331E-09 midg,1,midg; midg,igrid,midg 3.2454520E-10 2.9274042E-10 1,midg,midg; igrid,midg,midg -7.0640194E-10 7.0978945E-10 gauss-seidel spectral radius is 0.9832603 estimated iterations to convergence 64 setup time was (sec) 0.4300000 now iterating at: 14:00:14 rms-change max change #iterations 8.1599876E-02 13.81660 at 10iterations 5.8356519E-03 0.9817715 at 20iterations 4.7985755E-04 7.5830460E-02 at 30iterations 5.5928147E-05 1.0311127E-02 at 40iterations 9.1552411E-06 1.5964508E-03 at 50iterations finished qdiffx linear iterations at : 14:00:17 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 9.1552411E-06 1.5964508E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 14:00:18 3.476u 0.172s 0:04.58 79.4% 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 14:00:18 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 = 3101 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.664459 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): -9.530000 48.15900 ymin,ymax (A): -19.25300 29.61100 zmin,zma (A): -22.72800 41.43700 x,y,z range (A): 57.68900 48.86400 64.16500 scale (grids/A): 1.664459 object centre (A): 19.31450 5.179000 9.354500 number of atom coordinates read : 3101 total number of charged atoms : 2966 net assigned charge : 3.500005 assigned positive charge : 471.9679 centred at (gu) : 84.95531 87.35018 91.90945 assigned negative charge : -468.4690 centred at (gu) : 84.71880 87.33591 91.53065 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28833 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 21880 mr = 47115 m= 2512 mr = 14619 m= 70 mr = 1237 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 563 time to turn everything in is 0.3500000 number of dielectric boundary points 31403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 285 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 22835 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) : 0.5548196 object centre at (A) : 19.31450 5.179000 9.354500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6779172E-03 2.7150773E-02 midg,1,midg; midg,igrid,midg 6.7717052E-04 2.4349436E-03 1,midg,midg; igrid,midg,midg -7.6291179E-03 9.3501870E-04 gauss-seidel spectral radius is 0.9982741 estimated iterations to convergence 191 setup time was (sec) 0.5600000 now iterating at: 14:00:19 rms-change max change #iterations 3.559788 163.3475 at 10iterations 1.517810 57.06221 at 20iterations 0.6458712 25.62501 at 30iterations 0.2749895 9.681890 at 40iterations 0.1174633 3.941994 at 50iterations 5.0217163E-02 1.745524 at 60iterations 2.1302659E-02 0.7889093 at 70iterations 9.0857632E-03 0.3268108 at 80iterations 3.9103436E-03 0.1471825 at 90iterations 1.6810853E-03 5.9975624E-02 at 100iterations 7.2900107E-04 2.5749207E-02 at 110iterations 3.1986058E-04 1.0864258E-02 at 120iterations finished qdiffx linear iterations at : 14:00:26 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 3.1986058E-04 1.0864258E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 14:00:27 7.810u 0.236s 0:08.57 93.8% 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 Mon Oct 10 2011 at 14:00:27 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 = 3101 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: 2.496688 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): -9.530000 48.15900 ymin,ymax (A): -19.25300 29.61100 zmin,zma (A): -22.72800 41.43700 x,y,z range (A): 57.68900 48.86400 64.16500 scale (grids/A): 2.496688 object centre (A): 19.31450 5.179000 9.354500 number of atom coordinates read : 3101 total number of charged atoms : 2966 net assigned charge : 3.500005 assigned positive charge : 471.9679 centred at (gu) : 82.43259 86.02510 92.86404 assigned negative charge : -468.4690 centred at (gu) : 82.07811 86.00370 92.29589 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 162575 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28833 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 74884 mr = 115640 m= 21844 mr = 58520 m= 4097 mr = 15937 m= 322 mr = 2704 m= 6 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 2069 time to turn everything in is 0.8500000 number of dielectric boundary points 70803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 23703 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) : 1.664459 object centre at (A) : 19.31450 5.179000 9.354500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1453741 0.4364949 midg,1,midg; midg,igrid,midg -2.2002377E-02 3.3427875E-02 1,midg,midg; igrid,midg,midg -9.1858819E-02 -1.1250857E-02 gauss-seidel spectral radius is 0.9991695 estimated iterations to convergence 274 setup time was (sec) 1.080000 now iterating at: 14:00:28 rms-change max change #iterations 9.181767 297.6435 at 10iterations 5.219152 128.2308 at 20iterations 2.940390 67.81449 at 30iterations 1.653625 33.69913 at 40iterations 0.9250625 20.07638 at 50iterations 0.5178085 11.20632 at 60iterations 0.2891955 6.122740 at 70iterations 0.1611989 3.191521 at 80iterations 8.9757130E-02 1.828798 at 90iterations 4.9931984E-02 0.9831110 at 100iterations 2.7849467E-02 0.5646591 at 110iterations 1.5506068E-02 0.3036232 at 120iterations 8.6151641E-03 0.1831779 at 130iterations 4.7965022E-03 0.1038837 at 140iterations 2.6715535E-03 5.6696892E-02 at 150iterations 1.4881131E-03 2.9573441E-02 at 160iterations 8.3249441E-04 1.7074585E-02 at 170iterations 4.6711921E-04 9.5958710E-03 at 180iterations finished qdiffx linear iterations at : 14:00:40 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 4.6711921E-04 9.5958710E-03 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.21000 DelPhi exited at 14:00:41 13.209u 0.253s 0:13.79 97.5% 0+0k 0+0io 0pf+0w