Mon Oct 10 13:55:29 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 13:55:29 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2083 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: 0.7374570 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): -22.63900 25.63500 ymin,ymax (A): 9.026000 52.18700 zmin,zma (A): 20.82100 69.01400 x,y,z range (A): 48.27400 43.16100 48.19300 scale (grids/A): 0.7374570 object centre (A): 1.498000 30.60650 44.91750 number of atom coordinates read : 2083 total number of charged atoms : 1946 net assigned charge : -3.999990 assigned positive charge : 311.1719 centred at (gu) : 90.95155 89.74470 90.05564 assigned negative charge : -315.1721 centred at (gu) : 90.87532 89.70927 90.21304 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7738 nv = 96 ne = 84 npr = 43327 no. pairs analyzed = 43327 no. exposed pairs = 2630 no. arc points = 18547 no. surface atoms = 881 nbur = 1202 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 542 mr = 4328 m= 4 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 172 time to turn everything in is 0.2800000 number of dielectric boundary points 3846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1456 ## 112 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8185 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.9189242E-08 -2.2110956E-07 midg,1,midg; midg,igrid,midg -1.0571814E-07 -3.2153000E-08 1,midg,midg; igrid,midg,midg -1.1729060E-07 6.6109878E-09 gauss-seidel spectral radius is 0.9904155 estimated iterations to convergence 83 setup time was (sec) 0.5100000 now iterating at: 13:55:30 rms-change max change #iterations 0.2393429 31.31425 at 10iterations 3.2624278E-02 4.575485 at 20iterations 4.3386021E-03 0.6034241 at 30iterations 5.7867623E-04 7.9421997E-02 at 40iterations 7.7780089E-05 9.5596313E-03 at 50iterations finished qdiffx linear iterations at : 13:55:32 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 7.7780089E-05 9.5596313E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 13:55:33 3.317u 0.217s 0:03.90 90.2% 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 Mon Oct 10 2011 at 13:55:33 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2083 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: 2.212371 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): -22.63900 25.63500 ymin,ymax (A): 9.026000 52.18700 zmin,zma (A): 20.82100 69.01400 x,y,z range (A): 48.27400 43.16100 48.19300 scale (grids/A): 2.212371 object centre (A): 1.498000 30.60650 44.91750 number of atom coordinates read : 2083 total number of charged atoms : 1946 net assigned charge : -3.999990 assigned positive charge : 311.1719 centred at (gu) : 92.85459 89.23417 90.16695 assigned negative charge : -315.1721 centred at (gu) : 92.62583 89.12815 90.63931 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18547 grid for indexing accessible points = 1.400000 m= 32245 mr = 56214 m= 6964 mr = 24594 m= 763 mr = 4829 m= 32 mr = 407 m= 0 mr = 8 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 4074 time to turn everything in is 0.5900000 number of dielectric boundary points 35287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15487 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) : 0.7374570 object centre at (A) : 1.498000 30.60650 44.91750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9989790E-03 -9.8234497E-02 midg,1,midg; midg,igrid,midg -2.4172170E-02 -1.9250656E-02 1,midg,midg; igrid,midg,midg -3.1009335E-02 2.3312995E-02 gauss-seidel spectral radius is 0.9989172 estimated iterations to convergence 240 setup time was (sec) 0.8700000 now iterating at: 13:55:34 rms-change max change #iterations 4.987872 205.2417 at 10iterations 2.524483 83.65151 at 20iterations 1.287128 36.15071 at 30iterations 0.6515122 21.33900 at 40iterations 0.3318791 9.395605 at 50iterations 0.1685652 5.063186 at 60iterations 8.5712045E-02 2.505358 at 70iterations 4.3534745E-02 1.170317 at 80iterations 2.2232963E-02 0.6396918 at 90iterations 1.1254809E-02 0.3331385 at 100iterations 5.7407008E-03 0.1760697 at 110iterations 2.9097779E-03 8.6446762E-02 at 120iterations finished qdiffx linear iterations at : 13:55:41 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 2.9097779E-03 8.6446762E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 13:55:41 7.692u 0.234s 0:08.25 96.0% 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 13:55:41 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2083 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: 3.318557 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): -22.63900 25.63500 ymin,ymax (A): 9.026000 52.18700 zmin,zma (A): 20.82100 69.01400 x,y,z range (A): 48.27400 43.16100 48.19300 scale (grids/A): 3.318557 object centre (A): 1.498000 30.60650 44.91750 number of atom coordinates read : 2083 total number of charged atoms : 1946 net assigned charge : -3.999990 assigned positive charge : 311.1719 centred at (gu) : 94.28191 88.85120 90.25024 assigned negative charge : -315.1721 centred at (gu) : 93.93873 88.69222 90.95900 start vw surface at 0.1400000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 187360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18547 grid for indexing accessible points = 1.400000 m= 99343 mr = 135533 m= 42143 mr = 82413 m= 13382 mr = 34980 m= 3089 mr = 10610 m= 421 mr = 2362 m= 32 mr = 268 m= 3 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 14152 time to turn everything in is 2.020000 number of dielectric boundary points 79585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 15568 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) : 2.212371 object centre at (A) : 1.498000 30.60650 44.91750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4688213E-02 -0.9753538 midg,1,midg; midg,igrid,midg -9.9122830E-02 -0.2013739 1,midg,midg; igrid,midg,midg -0.3778447 0.1768603 gauss-seidel spectral radius is 0.9993155 estimated iterations to convergence 302 setup time was (sec) 2.320000 now iterating at: 13:55:44 rms-change max change #iterations 10.82119 323.2932 at 10iterations 6.350141 130.5587 at 20iterations 3.740506 85.29019 at 30iterations 2.196780 40.13409 at 40iterations 1.290933 21.27636 at 50iterations 0.7582482 12.52477 at 60iterations 0.4444808 7.569619 at 70iterations 0.2609312 4.115327 at 80iterations 0.1534209 2.835927 at 90iterations 8.9685768E-02 1.533968 at 100iterations 5.2722272E-02 0.8746910 at 110iterations 3.0853285E-02 0.5261297 at 120iterations 1.8140242E-02 0.3238697 at 130iterations 1.0635670E-02 0.1760893 at 140iterations 6.2232576E-03 0.1200714 at 150iterations 3.6589650E-03 6.1626434E-02 at 160iterations 2.1391662E-03 3.7539482E-02 at 170iterations 1.2576171E-03 2.3027420E-02 at 180iterations finished qdiffx linear iterations at : 13:55:54 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 1.2576171E-03 2.3027420E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 13:55:55 13.027u 0.261s 0:13.77 96.4% 0+0k 0+0io 0pf+0w