Sun Oct 9 08:13:56 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 Sun Oct 9 2011 at 08:13:56 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3475 !!! WARNING: NAP 1048 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5502658 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): -24.82200 22.37000 ymin,ymax (A): -22.06600 36.63400 zmin,zma (A): -17.01900 47.67700 x,y,z range (A): 47.19200 58.70000 64.69600 scale (grids/A): 0.5502658 object centre (A): -1.226001 7.284001 15.32900 number of atom coordinates read : 3475 total number of charged atoms : 3335 net assigned charge : 10.50003 assigned positive charge : 519.9734 centred at (gu) : 89.62482 87.03744 90.07648 assigned negative charge : -509.4751 centred at (gu) : 89.68015 87.05321 90.12054 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6947 nv = 96 ne = 84 npr = 69204 no. pairs analyzed = 69204 no. exposed pairs = 4438 no. arc points = 31598 no. surface atoms = 1479 nbur = 1996 mkacc time = 0.1500000 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= 311 mr = 3588 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3500000 number of dielectric boundary points 3658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3090 ## 366 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8969 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1234210E-09 3.7264580E-10 midg,1,midg; midg,igrid,midg 1.8487406E-09 3.1119238E-10 1,midg,midg; igrid,midg,midg 1.3612407E-09 2.4503360E-10 gauss-seidel spectral radius is 0.9830139 estimated iterations to convergence 63 setup time was (sec) 0.6000000 now iterating at: 08:13:57 rms-change max change #iterations 8.3071381E-02 13.29186 at 10iterations 5.8713160E-03 0.9209480 at 20iterations 5.5523199E-04 9.1184616E-02 at 30iterations 1.1032215E-04 1.4142156E-02 at 40iterations 2.9335437E-05 3.7164688E-03 at 50iterations finished qdiffx linear iterations at : 08:13:59 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 2.9335437E-05 3.7164688E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 08:14:00 3.416u 0.196s 0:03.94 91.3% 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 Sun Oct 9 2011 at 08:14:00 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3475 !!! WARNING: NAP 1048 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.650798 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): -24.82200 22.37000 ymin,ymax (A): -22.06600 36.63400 zmin,zma (A): -17.01900 47.67700 x,y,z range (A): 47.19200 58.70000 64.69600 scale (grids/A): 1.650798 object centre (A): -1.226001 7.284001 15.32900 number of atom coordinates read : 3475 total number of charged atoms : 3335 net assigned charge : 10.50003 assigned positive charge : 519.9734 centred at (gu) : 88.87370 81.11153 90.22854 assigned negative charge : -509.4751 centred at (gu) : 89.04038 81.15937 90.36147 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77246 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31598 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24585 mr = 52517 m= 2778 mr = 16852 m= 96 mr = 1367 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 819 time to turn everything in is 0.5700000 number of dielectric boundary points 33960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 348 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 25623 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) : 0.5502658 object centre at (A) : -1.226001 7.284001 15.32900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1220122E-02 -6.6251209E-04 midg,1,midg; midg,igrid,midg 2.0723125E-02 6.5004569E-03 1,midg,midg; igrid,midg,midg 1.5955521E-02 7.0475700E-04 gauss-seidel spectral radius is 0.9982834 estimated iterations to convergence 192 setup time was (sec) 0.9000000 now iterating at: 08:14:01 rms-change max change #iterations 3.699261 185.4449 at 10iterations 1.584009 57.26448 at 20iterations 0.6733007 22.39122 at 30iterations 0.2888568 10.11063 at 40iterations 0.1234878 4.008234 at 50iterations 5.2524898E-02 1.894147 at 60iterations 2.2552013E-02 0.7414246 at 70iterations 9.6879881E-03 0.3309784 at 80iterations 4.1617909E-03 0.1374989 at 90iterations 1.7890460E-03 5.8998108E-02 at 100iterations 7.7658478E-04 3.4009933E-02 at 110iterations 3.4291425E-04 1.2315750E-02 at 120iterations finished qdiffx linear iterations at : 08:14:08 total time elapsed so far: 8.380000 # loops : 120 mean,max change (kT/e) : 3.4291425E-04 1.2315750E-02 energy calculations done at 8.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.560000 DelPhi exited at 08:14:09 8.563u 0.281s 0:09.12 96.9% 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 Sun Oct 9 2011 at 08:14:09 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3475 !!! WARNING: NAP 1048 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.476196 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): -24.82200 22.37000 ymin,ymax (A): -22.06600 36.63400 zmin,zma (A): -17.01900 47.67700 x,y,z range (A): 47.19200 58.70000 64.69600 scale (grids/A): 2.476196 object centre (A): -1.226001 7.284001 15.32900 number of atom coordinates read : 3475 total number of charged atoms : 3335 net assigned charge : 10.50003 assigned positive charge : 519.9734 centred at (gu) : 88.31026 76.66705 90.34235 assigned negative charge : -509.4751 centred at (gu) : 88.56055 76.73894 90.54218 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 179697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31598 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 84009 mr = 128824 m= 24907 mr = 66215 m= 4305 mr = 18624 m= 340 mr = 2789 m= 10 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 2772 time to turn everything in is 1.370000 number of dielectric boundary points 76676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 26644 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) : 1.650798 object centre at (A) : -1.226001 7.284001 15.32900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2564985 -3.2096371E-02 midg,1,midg; midg,igrid,midg 0.4133678 0.1242040 1,midg,midg; igrid,midg,midg 0.2010074 -2.3465648E-02 gauss-seidel spectral radius is 0.9991834 estimated iterations to convergence 276 setup time was (sec) 1.700000 now iterating at: 08:14:11 rms-change max change #iterations 9.595952 318.4138 at 10iterations 5.542332 138.6756 at 20iterations 3.174429 82.99208 at 30iterations 1.811527 44.35797 at 40iterations 1.025327 25.30758 at 50iterations 0.5789297 14.11422 at 60iterations 0.3264425 7.450286 at 70iterations 0.1838043 4.316538 at 80iterations 0.1034623 2.392483 at 90iterations 5.7968352E-02 1.336185 at 100iterations 3.2524150E-02 0.7117653 at 110iterations 1.8256808E-02 0.3732605 at 120iterations 1.0224418E-02 0.2198296 at 130iterations 5.7238829E-03 0.1123638 at 140iterations 3.2121113E-03 6.1890602E-02 at 150iterations 1.7977529E-03 4.0761948E-02 at 160iterations 1.0056258E-03 2.1377087E-02 at 170iterations 5.6396046E-04 1.2779236E-02 at 180iterations finished qdiffx linear iterations at : 08:14:22 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 5.6396046E-04 1.2779236E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 08:14:23 12.937u 0.314s 0:13.57 97.5% 0+0k 0+0io 0pf+0w