Sun Oct 9 08:22:32 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+sph2.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 = amb2.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 08:22:32 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5714 !!! WARNING: HIR 1428 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5000913 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): -2.765000 68.42200 ymin,ymax (A): -28.39600 38.98300 zmin,zma (A): 24.50400 92.68100 x,y,z range (A): 71.18700 67.37900 68.17700 scale (grids/A): 0.5000913 object centre (A): 32.82850 5.293499 58.59250 number of atom coordinates read : 5714 total number of charged atoms : 5544 net assigned charge : -7.485940 assigned positive charge : 861.0891 centred at (gu) : 89.48570 91.02763 90.58517 assigned negative charge : -868.5817 centred at (gu) : 89.41348 91.02695 90.63371 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8910 nv = 96 ne = 84 npr = 115422 no. pairs analyzed = 115422 no. exposed pairs = 7077 no. arc points = 48615 no. surface atoms = 2380 nbur = 3334 mkacc time = 0.2500000 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 = 1.736000 m= 313 mr = 4621 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.5100000 number of dielectric boundary points 4593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4671 ## 704 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12016 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6704404E-11 -1.8910641E-10 midg,1,midg; midg,igrid,midg -5.0266818E-11 -8.2345436E-11 1,midg,midg; igrid,midg,midg -2.4073846E-10 6.7615066E-11 gauss-seidel spectral radius is 0.9796199 estimated iterations to convergence 58 setup time was (sec) 0.7400000 now iterating at: 08:22:33 rms-change max change #iterations 6.8635307E-02 10.38242 at 10iterations 4.4377656E-03 0.7782364 at 20iterations 7.6326338E-04 0.1799850 at 30iterations 2.3657506E-04 5.5187225E-02 at 40iterations 7.7167904E-05 1.7406464E-02 at 50iterations finished qdiffx linear iterations at : 08:22:36 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 7.7167904E-05 1.7406464E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 08:22:36 3.509u 0.186s 0:04.01 91.7% 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 08:22:36 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5714 !!! WARNING: HIR 1428 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2000000 grid size : 179 scale,in grids/A, set to be: 1.500274 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): -2.765000 68.42200 ymin,ymax (A): -28.39600 38.98300 zmin,zma (A): 24.50400 92.68100 x,y,z range (A): 71.18700 67.37900 68.17700 scale (grids/A): 1.500274 object centre (A): 32.82850 5.293499 58.59250 number of atom coordinates read : 5714 total number of charged atoms : 5544 net assigned charge : -7.485940 assigned positive charge : 861.0891 centred at (gu) : 88.45586 93.08174 91.75388 assigned negative charge : -868.5817 centred at (gu) : 88.24004 93.08090 91.90102 start vw surface at 0.2600000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 102098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48615 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 28363 mr = 70408 m= 2259 mr = 18431 m= 40 mr = 951 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1059 time to turn everything in is 0.7500000 number of dielectric boundary points 42970 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 668 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 41290 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) : 0.5000913 object centre at (A) : 32.82850 5.293499 58.59250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4103403E-03 -1.1875457E-02 midg,1,midg; midg,igrid,midg -7.0269727E-03 -6.6012964E-03 1,midg,midg; igrid,midg,midg -8.8835098E-03 1.7622489E-02 gauss-seidel spectral radius is 0.9981092 estimated iterations to convergence 183 setup time was (sec) 1.030000 now iterating at: 08:22:38 rms-change max change #iterations 4.046251 148.3443 at 10iterations 1.662482 62.61078 at 20iterations 0.6782255 21.06185 at 30iterations 0.2785167 8.642577 at 40iterations 0.1145148 3.678772 at 50iterations 4.7083981E-02 1.438107 at 60iterations 1.9435227E-02 0.6173806 at 70iterations 8.0912421E-03 0.2477112 at 80iterations 3.4022781E-03 0.1077561 at 90iterations 1.4857763E-03 5.0163269E-02 at 100iterations 6.8571721E-04 2.6581764E-02 at 110iterations 3.4991911E-04 1.6662598E-02 at 120iterations finished qdiffx linear iterations at : 08:22:44 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 3.4991911E-04 1.6662598E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 08:22:45 7.992u 0.247s 0:08.54 96.3% 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 08:22:45 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5714 !!! WARNING: HIR 1428 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.250411 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): -2.765000 68.42200 ymin,ymax (A): -28.39600 38.98300 zmin,zma (A): 24.50400 92.68100 x,y,z range (A): 71.18700 67.37900 68.17700 scale (grids/A): 2.250411 object centre (A): 32.82850 5.293499 58.59250 number of atom coordinates read : 5714 total number of charged atoms : 5544 net assigned charge : -7.485940 assigned positive charge : 861.0891 centred at (gu) : 87.68353 94.62196 92.63069 assigned negative charge : -868.5817 centred at (gu) : 87.35983 94.62114 92.85146 start vw surface at 0.2400000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 237790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48615 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 103781 mr = 172867 m= 24531 mr = 80167 m= 3173 mr = 17505 m= 135 mr = 1959 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.9899999 no. cavity mid-points inaccessible to solvent = 3485 time to turn everything in is 1.710000 number of dielectric boundary points 96883 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 44195 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) : 1.500274 object centre at (A) : 32.82850 5.293499 58.59250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2142230 -0.2801489 midg,1,midg; midg,igrid,midg -8.6177140E-02 -0.1791721 1,midg,midg; igrid,midg,midg 4.7461733E-02 0.4386165 gauss-seidel spectral radius is 0.9991888 estimated iterations to convergence 277 setup time was (sec) 2.030000 now iterating at: 08:22:47 rms-change max change #iterations 11.17524 299.5452 at 10iterations 6.475090 144.2409 at 20iterations 3.739040 88.55356 at 30iterations 2.140716 50.16956 at 40iterations 1.224041 23.12677 at 50iterations 0.6978838 14.06890 at 60iterations 0.3957869 7.479605 at 70iterations 0.2244178 4.246495 at 80iterations 0.1269418 2.413597 at 90iterations 7.1747236E-02 1.309019 at 100iterations 4.0488500E-02 0.6778021 at 110iterations 2.2793474E-02 0.4350553 at 120iterations 1.2867137E-02 0.2180157 at 130iterations 7.2551244E-03 0.1400914 at 140iterations 4.0944889E-03 7.6556206E-02 at 150iterations 2.3208670E-03 3.8232803E-02 at 160iterations 1.3136794E-03 2.2855759E-02 at 170iterations 7.5216201E-04 1.2615204E-02 at 180iterations finished qdiffx linear iterations at : 08:22:58 total time elapsed so far: 13.26000 # loops : 180 mean,max change (kT/e) : 7.5216201E-04 1.2615204E-02 energy calculations done at 13.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.44000 DelPhi exited at 08:22:59 13.447u 0.247s 0:13.97 97.9% 0+0k 0+0io 0pf+0w