Sat Oct 8 19:01:11 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 Sat Oct 8 2011 at 19:01:11 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 = 2605 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6378556 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): -32.29800 17.52900 ymin,ymax (A): -23.68000 23.06500 zmin,zma (A): -12.64800 43.16400 x,y,z range (A): 49.82700 46.74500 55.81200 scale (grids/A): 0.6378556 object centre (A): -7.384501 -0.3074999 15.25800 number of atom coordinates read : 2605 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 88.68768 89.19125 90.32104 assigned negative charge : -390.0956 centred at (gu) : 88.57587 89.22629 90.21053 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7042 nv = 96 ne = 84 npr = 53933 no. pairs analyzed = 53933 no. exposed pairs = 3068 no. arc points = 22018 no. surface atoms = 1033 nbur = 1572 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 378 mr = 3972 m= 3 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2163 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8467 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6406959E-09 1.9613967E-08 midg,1,midg; midg,igrid,midg 1.2010577E-08 2.0474782E-09 1,midg,midg; igrid,midg,midg -8.4450757E-09 1.3942935E-08 gauss-seidel spectral radius is 0.9872645 estimated iterations to convergence 72 setup time was (sec) 0.6400000 now iterating at: 19:01:12 rms-change max change #iterations 0.1435113 20.29132 at 10iterations 1.4380447E-02 2.002381 at 20iterations 1.4004289E-03 0.2014008 at 30iterations 1.4183749E-04 1.7857552E-02 at 40iterations 1.3601409E-05 1.8444061E-03 at 50iterations finished qdiffx linear iterations at : 19:01:16 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 1.3601409E-05 1.8444061E-03 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 19:01:16 4.355u 0.289s 0:05.03 92.0% 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 Sat Oct 8 2011 at 19:01:16 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 = 2605 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.913567 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): -32.29800 17.52900 ymin,ymax (A): -23.68000 23.06500 zmin,zma (A): -12.64800 43.16400 x,y,z range (A): 49.82700 46.74500 55.81200 scale (grids/A): 1.913567 object centre (A): -7.384501 -0.3074999 15.25800 number of atom coordinates read : 2605 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 86.06240 87.57322 90.96268 assigned negative charge : -390.0956 centred at (gu) : 85.72748 87.67860 90.63114 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76040 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22018 grid for indexing accessible points = 1.400000 m= 27817 mr = 53511 m= 4437 mr = 20796 m= 252 mr = 2786 m= 1 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1542 time to turn everything in is 0.6600000 number of dielectric boundary points 31361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 19438 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) : 0.6378556 object centre at (A) : -7.384501 -0.3074999 15.25800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5959656E-02 3.1083697E-02 midg,1,midg; midg,igrid,midg 1.5591958E-02 1.1953069E-03 1,midg,midg; igrid,midg,midg -7.2313668E-03 4.1664433E-02 gauss-seidel spectral radius is 0.9986473 estimated iterations to convergence 215 setup time was (sec) 1.010000 now iterating at: 19:01:18 rms-change max change #iterations 4.292168 179.4585 at 10iterations 2.022036 70.79788 at 20iterations 0.9494082 31.73512 at 30iterations 0.4466484 16.45737 at 40iterations 0.2089056 6.717358 at 50iterations 9.8339438E-02 3.284042 at 60iterations 4.6184938E-02 1.632606 at 70iterations 2.1786613E-02 0.6851387 at 80iterations 1.0201850E-02 0.3169327 at 90iterations 4.8071276E-03 0.1582184 at 100iterations 2.2597697E-03 7.6322556E-02 at 110iterations 1.0644587E-03 3.5232544E-02 at 120iterations finished qdiffx linear iterations at : 19:01:27 total time elapsed so far: 9.870000 # loops : 120 mean,max change (kT/e) : 1.0644587E-03 3.5232544E-02 energy calculations done at 9.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.06000 DelPhi exited at 19:01:27 10.065u 0.303s 0:10.63 97.4% 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 Sat Oct 8 2011 at 19:01:27 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 = 2605 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.870350 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): -32.29800 17.52900 ymin,ymax (A): -23.68000 23.06500 zmin,zma (A): -12.64800 43.16400 x,y,z range (A): 49.82700 46.74500 55.81200 scale (grids/A): 2.870350 object centre (A): -7.384501 -0.3074999 15.25800 number of atom coordinates read : 2605 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 84.09348 86.35965 91.44387 assigned negative charge : -390.0956 centred at (gu) : 83.59127 86.51784 90.94673 start vw surface at 0.1500000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 175991 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22018 grid for indexing accessible points = 1.400000 m= 89966 mr = 129208 m= 32393 mr = 74544 m= 7846 mr = 26202 m= 1173 mr = 5908 m= 94 mr = 766 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 4990 time to turn everything in is 1.520000 number of dielectric boundary points 70785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 19728 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) : 1.913567 object centre at (A) : -7.384501 -0.3074999 15.25800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1507247E-02 0.4545342 midg,1,midg; midg,igrid,midg 0.1804260 -3.4963839E-02 1,midg,midg; igrid,midg,midg -2.2622643E-02 0.4585378 gauss-seidel spectral radius is 0.9992562 estimated iterations to convergence 289 setup time was (sec) 1.900000 now iterating at: 19:01:29 rms-change max change #iterations 9.934038 348.4258 at 10iterations 5.731787 118.5031 at 20iterations 3.290797 68.89465 at 30iterations 1.891066 34.27952 at 40iterations 1.087140 19.45179 at 50iterations 0.6236289 11.41467 at 60iterations 0.3578579 6.083267 at 70iterations 0.2052314 3.763561 at 80iterations 0.1178005 2.102017 at 90iterations 6.7464523E-02 1.166023 at 100iterations 3.8678221E-02 0.7008543 at 110iterations 2.2154652E-02 0.4012280 at 120iterations 1.2670835E-02 0.2243080 at 130iterations 7.2798766E-03 0.1313212 at 140iterations 4.1764872E-03 7.3049545E-02 at 150iterations 2.3964979E-03 4.2519987E-02 at 160iterations 1.3708874E-03 2.5296211E-02 at 170iterations 7.8721187E-04 1.4194489E-02 at 180iterations finished qdiffx linear iterations at : 19:01:44 total time elapsed so far: 16.39000 # loops : 180 mean,max change (kT/e) : 7.8721187E-04 1.4194489E-02 energy calculations done at 16.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.56000 DelPhi exited at 19:01:44 16.561u 0.331s 0:17.16 98.4% 0+0k 0+0io 0pf+0w