Mon Oct 10 14:18:01 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 14:18:01 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 = 2646 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5717223 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): -16.12900 38.81200 ymin,ymax (A): 28.70500 75.27600 zmin,zma (A): -10.73800 51.53000 x,y,z range (A): 54.94100 46.57100 62.26800 scale (grids/A): 0.5717223 object centre (A): 11.34150 51.99050 20.39600 number of atom coordinates read : 2646 total number of charged atoms : 2496 net assigned charge : -1.999992 assigned positive charge : 385.7266 centred at (gu) : 90.30031 91.14079 90.66496 assigned negative charge : -387.7274 centred at (gu) : 90.32140 91.12120 90.66036 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5598 nv = 96 ne = 84 npr = 53971 no. pairs analyzed = 53971 no. exposed pairs = 3464 no. arc points = 24007 no. surface atoms = 1172 nbur = 1474 mkacc time = 0.1800000 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 = 1.484000 m= 255 mr = 2819 m= 3 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3025 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2469 ## 270 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7236 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3937411E-10 -3.0526698E-10 midg,1,midg; midg,igrid,midg -4.7028803E-10 -5.4075133E-11 1,midg,midg; igrid,midg,midg -2.2982500E-11 -6.8269757E-10 gauss-seidel spectral radius is 0.9841876 estimated iterations to convergence 65 setup time was (sec) 0.6900000 now iterating at: 14:18:02 rms-change max change #iterations 8.6490877E-02 14.47816 at 10iterations 6.3620540E-03 1.076868 at 20iterations 5.2920158E-04 8.1008911E-02 at 30iterations 8.3764215E-05 1.9615173E-02 at 40iterations 2.6631793E-05 6.7205429E-03 at 50iterations finished qdiffx linear iterations at : 14:18:06 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 2.6631793E-05 6.7205429E-03 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 14:18:07 4.569u 0.406s 0:05.47 90.6% 0+0k 0+0io 5pf+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 14:18:07 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 = 2646 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.715167 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): -16.12900 38.81200 ymin,ymax (A): 28.70500 75.27600 zmin,zma (A): -10.73800 51.53000 x,y,z range (A): 54.94100 46.57100 62.26800 scale (grids/A): 1.715167 object centre (A): 11.34150 51.99050 20.39600 number of atom coordinates read : 2646 total number of charged atoms : 2496 net assigned charge : -1.999992 assigned positive charge : 385.7266 centred at (gu) : 90.90039 93.42173 91.99447 assigned negative charge : -387.7274 centred at (gu) : 90.96379 93.36312 91.98087 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 61551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24007 grid for indexing accessible points = 1.400000 m= 19133 mr = 40939 m= 2116 mr = 12998 m= 67 mr = 1008 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 27909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19291 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) : 0.5717223 object centre at (A) : 11.34150 51.99050 20.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2279475E-03 -2.2397734E-02 midg,1,midg; midg,igrid,midg 3.3669788E-04 -2.8942630E-03 1,midg,midg; igrid,midg,midg -3.7137573E-03 -4.0367716E-03 gauss-seidel spectral radius is 0.9983228 estimated iterations to convergence 194 setup time was (sec) 0.9600000 now iterating at: 14:18:08 rms-change max change #iterations 3.378963 153.9689 at 10iterations 1.448619 53.32167 at 20iterations 0.6262059 22.88447 at 30iterations 0.2685543 9.323573 at 40iterations 0.1160849 4.231505 at 50iterations 4.9801823E-02 2.018350 at 60iterations 2.1606334E-02 0.8023934 at 70iterations 9.3211187E-03 0.3672047 at 80iterations 4.0807715E-03 0.1510353 at 90iterations 1.8104708E-03 7.4106693E-02 at 100iterations 8.3658402E-04 3.7949562E-02 at 110iterations 4.1946024E-04 1.9433975E-02 at 120iterations finished qdiffx linear iterations at : 14:18:17 total time elapsed so far: 10.07000 # loops : 120 mean,max change (kT/e) : 4.1946024E-04 1.9433975E-02 energy calculations done at 10.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.29000 DelPhi exited at 14:18:18 10.296u 0.462s 0:11.07 97.1% 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 14:18:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2646 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.572750 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): -16.12900 38.81200 ymin,ymax (A): 28.70500 75.27600 zmin,zma (A): -10.73800 51.53000 x,y,z range (A): 54.94100 46.57100 62.26800 scale (grids/A): 2.572750 object centre (A): 11.34150 51.99050 20.39600 number of atom coordinates read : 2646 total number of charged atoms : 2496 net assigned charge : -1.999992 assigned positive charge : 385.7266 centred at (gu) : 91.35030 95.13239 92.99141 assigned negative charge : -387.7274 centred at (gu) : 91.44576 95.04480 92.97124 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 143026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24007 grid for indexing accessible points = 1.400000 m= 65200 mr = 100642 m= 19320 mr = 51147 m= 3326 mr = 14185 m= 274 mr = 2103 m= 7 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.580000 number of dielectric boundary points 62949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 19958 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) : 1.715167 object centre at (A) : 11.34150 51.99050 20.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8227262E-02 -0.1739484 midg,1,midg; midg,igrid,midg 1.6317576E-02 -8.7239988E-02 1,midg,midg; igrid,midg,midg -9.4902888E-02 -8.1623510E-02 gauss-seidel spectral radius is 0.9991728 estimated iterations to convergence 275 setup time was (sec) 1.930000 now iterating at: 14:18:20 rms-change max change #iterations 8.498841 296.6384 at 10iterations 4.811347 126.8002 at 20iterations 2.707667 70.00182 at 30iterations 1.518731 33.13020 at 40iterations 0.8493510 20.14762 at 50iterations 0.4746689 10.81767 at 60iterations 0.2650377 5.862137 at 70iterations 0.1481148 3.319296 at 80iterations 8.2589783E-02 2.109636 at 90iterations 4.5845490E-02 1.051939 at 100iterations 2.5547989E-02 0.6153870 at 110iterations 1.4242067E-02 0.2770834 at 120iterations 7.9189688E-03 0.1708784 at 130iterations 4.4156322E-03 0.1002862 at 140iterations 2.4506368E-03 4.9979210E-02 at 150iterations 1.3648149E-03 2.7763367E-02 at 160iterations 7.5829821E-04 1.6227722E-02 at 170iterations 4.2232536E-04 8.8281631E-03 at 180iterations finished qdiffx linear iterations at : 14:18:35 total time elapsed so far: 16.58000 # loops : 180 mean,max change (kT/e) : 4.2232536E-04 8.8281631E-03 energy calculations done at 16.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.80000 DelPhi exited at 14:18:36 16.802u 0.465s 0:17.93 96.2% 0+0k 0+0io 0pf+0w