Mon Oct 10 10:42:09 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 Mon Oct 10 2011 at 10:42:09 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5296 !!! WARNING: HIR 300 has a net charge of 0.5140 !!! WARNING: ADP 1585 has a net charge of -2.0000 !!! WARNING: ADP 1587 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5233370 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): -26.93900 40.13000 ymin,ymax (A): -43.85600 24.16900 zmin,zma (A): -36.31500 26.99500 x,y,z range (A): 67.06900 68.02500 63.31000 scale (grids/A): 0.5233370 object centre (A): 6.595501 -9.843499 -4.660000 number of atom coordinates read : 5296 total number of charged atoms : 5140 net assigned charge : 6.514019 assigned positive charge : 844.8027 centred at (gu) : 89.28020 90.95844 90.41363 assigned negative charge : -838.2968 centred at (gu) : 89.27753 90.90432 90.38882 start vw surface at 0.2300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 9344 nv = 96 ne = 84 npr = 105231 no. pairs analyzed = 105231 no. exposed pairs = 6358 no. arc points = 42250 no. surface atoms = 2140 nbur = 3156 mkacc time = 0.3000000 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 = 1.624000 m= 352 mr = 5225 m= 0 mr = 9 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 4462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4287 ## 581 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 12417 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6227298E-11 3.1695091E-10 midg,1,midg; midg,igrid,midg -9.5873795E-11 5.5786487E-10 1,midg,midg; igrid,midg,midg 1.7165297E-10 1.4285541E-10 gauss-seidel spectral radius is 0.9813562 estimated iterations to convergence 60 setup time was (sec) 0.8700000 now iterating at: 10:42:10 rms-change max change #iterations 8.3579041E-02 13.96134 at 10iterations 5.3102756E-03 0.7322617 at 20iterations 5.8851478E-04 0.1106567 at 30iterations 1.7106510E-04 3.6678314E-02 at 40iterations 5.9239119E-05 1.2685776E-02 at 50iterations finished qdiffx linear iterations at : 10:42:14 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 5.9239119E-05 1.2685776E-02 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 10:42:14 4.343u 0.262s 0:04.88 94.2% 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 10:42:14 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 # of charge parameter records: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5296 !!! WARNING: HIR 300 has a net charge of 0.5140 !!! WARNING: ADP 1585 has a net charge of -2.0000 !!! WARNING: ADP 1587 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.570011 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): -26.93900 40.13000 ymin,ymax (A): -43.85600 24.16900 zmin,zma (A): -36.31500 26.99500 x,y,z range (A): 67.06900 68.02500 63.31000 scale (grids/A): 1.570011 object centre (A): 6.595501 -9.843499 -4.660000 number of atom coordinates read : 5296 total number of charged atoms : 5140 net assigned charge : 6.514019 assigned positive charge : 844.8027 centred at (gu) : 87.83879 92.87369 91.23927 assigned negative charge : -838.2968 centred at (gu) : 87.83272 92.71277 91.16668 start vw surface at 0.2400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 106448 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42250 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 33711 mr = 76634 m= 3108 mr = 23873 m= 65 mr = 1419 m= 0 mr = 4 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 549 time to turn everything in is 0.9300000 number of dielectric boundary points 41402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 592 ## 12 charges are in solution ## iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 38865 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) : 0.5233370 object centre at (A) : 6.595501 -9.843499 -4.660000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7200324E-03 -3.6848788E-04 midg,1,midg; midg,igrid,midg -3.3689879E-02 1.5497706E-02 1,midg,midg; igrid,midg,midg -9.3611833E-03 1.9915191E-02 gauss-seidel spectral radius is 0.9982518 estimated iterations to convergence 190 setup time was (sec) 1.230000 now iterating at: 10:42:16 rms-change max change #iterations 4.413389 169.4002 at 10iterations 1.873924 55.17670 at 20iterations 0.7976024 24.05190 at 30iterations 0.3387923 10.07521 at 40iterations 0.1438674 4.312421 at 50iterations 6.1163168E-02 1.978765 at 60iterations 2.6127445E-02 0.8598404 at 70iterations 1.1148272E-02 0.3499126 at 80iterations 4.7715767E-03 0.1372719 at 90iterations 2.0671997E-03 6.7214966E-02 at 100iterations 9.1693189E-04 2.8800964E-02 at 110iterations 4.2937521E-04 1.6510010E-02 at 120iterations finished qdiffx linear iterations at : 10:42:24 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 4.2937521E-04 1.6510010E-02 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.840000 DelPhi exited at 10:42:24 9.840u 0.290s 0:10.40 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 Mon Oct 10 2011 at 10:42:24 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5296 !!! WARNING: HIR 300 has a net charge of 0.5140 !!! WARNING: ADP 1585 has a net charge of -2.0000 !!! WARNING: ADP 1587 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.355016 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): -26.93900 40.13000 ymin,ymax (A): -43.85600 24.16900 zmin,zma (A): -36.31500 26.99500 x,y,z range (A): 67.06900 68.02500 63.31000 scale (grids/A): 2.355016 object centre (A): 6.595501 -9.843499 -4.660000 number of atom coordinates read : 5296 total number of charged atoms : 5140 net assigned charge : 6.514019 assigned positive charge : 844.8027 centred at (gu) : 86.75787 94.31010 91.85835 assigned negative charge : -838.2968 centred at (gu) : 86.74904 94.06906 91.75001 start vw surface at 0.2200000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 247494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42250 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 119397 mr = 186597 m= 32383 mr = 96766 m= 4621 mr = 24401 m= 242 mr = 2982 m= 2 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 1.450000 no. cavity mid-points inaccessible to solvent = 1799 time to turn everything in is 2.310000 number of dielectric boundary points 93311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 2.470000 number of grid points assigned charge 41033 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) : 1.570011 object centre at (A) : 6.595501 -9.843499 -4.660000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1131097E-02 -6.6565886E-02 midg,1,midg; midg,igrid,midg -0.7447411 0.2109214 1,midg,midg; igrid,midg,midg -0.3048356 0.4257212 gauss-seidel spectral radius is 0.9992055 estimated iterations to convergence 280 setup time was (sec) 2.640000 now iterating at: 10:42:27 rms-change max change #iterations 11.69886 315.8795 at 10iterations 6.814899 152.4494 at 20iterations 3.933962 85.13796 at 30iterations 2.259768 43.50647 at 40iterations 1.291371 23.61803 at 50iterations 0.7383070 13.64730 at 60iterations 0.4194668 8.008200 at 70iterations 0.2380639 4.168954 at 80iterations 0.1348034 2.519567 at 90iterations 7.6556183E-02 1.270260 at 100iterations 4.3260861E-02 0.7286072 at 110iterations 2.4494834E-02 0.3984985 at 120iterations 1.3854863E-02 0.2610974 at 130iterations 7.8582512E-03 0.1297073 at 140iterations 4.4527049E-03 6.9274902E-02 at 150iterations 2.5332363E-03 4.2259216E-02 at 160iterations 1.4498847E-03 2.5545120E-02 at 170iterations 8.4080070E-04 1.4764786E-02 at 180iterations finished qdiffx linear iterations at : 10:42:42 total time elapsed so far: 16.86000 # loops : 180 mean,max change (kT/e) : 8.4080070E-04 1.4764786E-02 energy calculations done at 16.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.04000 DelPhi exited at 10:42:42 17.040u 0.321s 0:17.66 98.3% 0+0k 0+0io 0pf+0w