Wed Feb 15 08:57:02 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:57:02 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 ! Automatically converted from prot.table.ambcrg.ambH by pro # of charge parameter records: 1051 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 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: 0.4994389 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): -9.632999 38.48400 ymin,ymax (A): -52.31200 12.73300 zmin,zma (A): 20.09300 91.37300 x,y,z range (A): 48.11700 65.04500 71.28000 scale (grids/A): 0.4994389 object centre (A): 14.42550 -19.78950 55.73300 number of atom coordinates read : 2960 total number of charged atoms : 2825 net assigned charge : 9.500021 assigned positive charge : 418.0813 centred at (gu) : 91.30943 94.90833 89.22078 assigned negative charge : -408.5823 centred at (gu) : 91.26785 94.98487 89.87395 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 4807 nv = 96 ne = 84 npr = 59927 no. pairs analyzed = 59927 no. exposed pairs = 4279 no. arc points = 30494 no. surface atoms = 1434 nbur = 1526 mkacc time = 0.1400000 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 = 1.680000 m= 167 mr = 2005 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 2968 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2858 ## 372 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6272 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4459516E-10 -4.4266119E-10 midg,1,midg; midg,igrid,midg 4.0604669E-11 2.3541613E-11 1,midg,midg; igrid,midg,midg 3.0094389E-11 1.6244008E-10 gauss-seidel spectral radius is 0.9793876 estimated iterations to convergence 58 setup time was (sec) 0.5700000 now iterating at: 08:57:03 rms-change max change #iterations 4.1789830E-02 10.10684 at 10iterations 2.3151438E-03 0.4190407 at 20iterations 2.2437696E-04 3.9649963E-02 at 30iterations 4.5819419E-05 8.0603361E-03 at 40iterations 1.0657392E-05 1.8982887E-03 at 50iterations finished qdiffx linear iterations at : 08:57:05 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.0657392E-05 1.8982887E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 08:57:06 3.375u 0.155s 0:03.87 90.9% 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 Wed Feb 15 2012 at 08:57:06 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 ! Automatically converted from prot.table.ambcrg.ambH by pro # of charge parameter records: 1051 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 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: 1.498317 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): -9.632999 38.48400 ymin,ymax (A): -52.31200 12.73300 zmin,zma (A): 20.09300 91.37300 x,y,z range (A): 48.11700 65.04500 71.28000 scale (grids/A): 1.498317 object centre (A): 14.42550 -19.78950 55.73300 number of atom coordinates read : 2960 total number of charged atoms : 2825 net assigned charge : 9.500021 assigned positive charge : 418.0813 centred at (gu) : 93.92752 104.7242 87.66168 assigned negative charge : -408.5823 centred at (gu) : 93.80348 104.9542 89.62164 start vw surface at 0.1700000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 52903 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30494 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 13638 mr = 31689 m= 1143 mr = 7972 m= 22 mr = 412 m= 1 mr = 1 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 0.4500000 number of dielectric boundary points 27633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 316 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 21114 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) : 0.4994389 object centre at (A) : 14.42550 -19.78950 55.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9534278E-02 -2.6342103E-02 midg,1,midg; midg,igrid,midg 1.9404670E-03 5.2146437E-03 1,midg,midg; igrid,midg,midg -5.4756517E-04 1.7084996E-03 gauss-seidel spectral radius is 0.9978020 estimated iterations to convergence 170 setup time was (sec) 0.7500000 now iterating at: 08:57:07 rms-change max change #iterations 2.561419 161.5906 at 10iterations 0.9650148 44.69133 at 20iterations 0.3647650 16.95522 at 30iterations 0.1390292 6.435225 at 40iterations 5.2879009E-02 2.152100 at 50iterations 2.0036895E-02 0.9008402 at 60iterations 7.6758810E-03 0.3222563 at 70iterations 2.9275867E-03 0.1218357 at 80iterations 1.1289046E-03 4.8809528E-02 at 90iterations 4.4117670E-04 1.9129753E-02 at 100iterations 1.7752554E-04 6.8788528E-03 at 110iterations 7.4383577E-05 2.9869080E-03 at 120iterations finished qdiffx linear iterations at : 08:57:14 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 7.4383577E-05 2.9869080E-03 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 08:57:14 7.676u 0.285s 0:08.38 94.8% 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 Wed Feb 15 2012 at 08:57:14 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 ! Automatically converted from prot.table.ambcrg.ambH by pro # of charge parameter records: 1051 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 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: 2.247475 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): -9.632999 38.48400 ymin,ymax (A): -52.31200 12.73300 zmin,zma (A): 20.09300 91.37300 x,y,z range (A): 48.11700 65.04500 71.28000 scale (grids/A): 2.247475 object centre (A): 14.42550 -19.78950 55.73300 number of atom coordinates read : 2960 total number of charged atoms : 2825 net assigned charge : 9.500021 assigned positive charge : 418.0813 centred at (gu) : 95.89114 112.0861 86.49230 assigned negative charge : -408.5823 centred at (gu) : 95.70511 112.4313 89.43230 start vw surface at 0.1500000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 122886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30494 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 48732 mr = 79201 m= 11879 mr = 34936 m= 1534 mr = 7802 m= 77 mr = 855 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 62302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 46 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 22533 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) : 1.498317 object centre at (A) : 14.42550 -19.78950 55.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.085103 -0.4812558 midg,1,midg; midg,igrid,midg 2.5844660E-02 2.5338823E-02 1,midg,midg; igrid,midg,midg -4.4610505E-03 1.4218240E-02 gauss-seidel spectral radius is 0.9989803 estimated iterations to convergence 248 setup time was (sec) 1.280000 now iterating at: 08:57:16 rms-change max change #iterations 7.090699 272.2032 at 10iterations 3.808831 100.9456 at 20iterations 2.022470 57.08311 at 30iterations 1.068196 29.04540 at 40iterations 0.5626037 14.94210 at 50iterations 0.2961422 8.190449 at 60iterations 0.1552766 4.357729 at 70iterations 8.1464492E-02 1.976248 at 80iterations 4.2538714E-02 1.173880 at 90iterations 2.2238713E-02 0.5307684 at 100iterations 1.1627253E-02 0.3087130 at 110iterations 6.0669542E-03 0.1489925 at 120iterations 3.1672406E-03 8.4016800E-02 at 130iterations 1.6542549E-03 3.7757874E-02 at 140iterations 8.6621928E-04 2.1634817E-02 at 150iterations 4.5592792E-04 1.1867523E-02 at 160iterations 2.4112021E-04 5.8364868E-03 at 170iterations 1.2859861E-04 3.1228065E-03 at 180iterations finished qdiffx linear iterations at : 08:57:26 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 1.2859861E-04 3.1228065E-03 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 08:57:27 11.810u 0.235s 0:12.34 97.5% 0+0k 0+0io 0pf+0w