Mon Oct 10 17:06:23 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 17:06:23 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2682 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: 0.5542840 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): -40.49500 6.727000 ymin,ymax (A): -9.829000 41.69500 zmin,zma (A): -61.76200 2.465000 x,y,z range (A): 47.22200 51.52400 64.22701 scale (grids/A): 0.5542840 object centre (A): -16.88400 15.93300 -29.64850 number of atom coordinates read : 2682 total number of charged atoms : 2543 net assigned charge : 6.000023 assigned positive charge : 403.2636 centred at (gu) : 89.68571 89.70136 90.59127 assigned negative charge : -397.2646 centred at (gu) : 89.65805 89.60868 90.52841 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5356 nv = 96 ne = 84 npr = 53569 no. pairs analyzed = 53569 no. exposed pairs = 3650 no. arc points = 25892 no. surface atoms = 1229 nbur = 1453 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 = 1.540000 m= 234 mr = 2601 m= 1 mr = 6 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 0.3000000 number of dielectric boundary points 2984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2656 ## 375 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7036 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6869405E-12 1.1757836E-09 midg,1,midg; midg,igrid,midg -2.6168193E-10 1.1663644E-09 1,midg,midg; igrid,midg,midg 3.1293823E-10 6.8392725E-10 gauss-seidel spectral radius is 0.9831951 estimated iterations to convergence 63 setup time was (sec) 0.5400000 now iterating at: 17:06:24 rms-change max change #iterations 7.4265271E-02 13.53101 at 10iterations 5.2194796E-03 0.9742994 at 20iterations 3.6403799E-04 6.0298443E-02 at 30iterations 2.7816659E-05 4.7936440E-03 at 40iterations 2.5617053E-06 5.0354004E-04 at 50iterations finished qdiffx linear iterations at : 17:06:27 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 2.5617053E-06 5.0354004E-04 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 17:06:28 3.914u 0.387s 0:04.65 92.2% 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 17:06:28 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2682 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: 1.662852 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): -40.49500 6.727000 ymin,ymax (A): -9.829000 41.69500 zmin,zma (A): -61.76200 2.465000 x,y,z range (A): 47.22200 51.52400 64.22701 scale (grids/A): 1.662852 object centre (A): -16.88400 15.93300 -29.64850 number of atom coordinates read : 2682 total number of charged atoms : 2543 net assigned charge : 6.000023 assigned positive charge : 403.2636 centred at (gu) : 89.05642 89.10346 91.77306 assigned negative charge : -397.2646 centred at (gu) : 88.97418 88.82572 91.58524 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25892 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17481 mr = 38781 m= 1727 mr = 11352 m= 52 mr = 765 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 27913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 19580 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) : 0.5542840 object centre at (A) : -16.88400 15.93300 -29.64850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3215560E-02 1.8301066E-02 midg,1,midg; midg,igrid,midg -9.5935743E-03 2.6596391E-03 1,midg,midg; igrid,midg,midg 4.0931950E-04 6.7447857E-03 gauss-seidel spectral radius is 0.9982259 estimated iterations to convergence 189 setup time was (sec) 0.7700000 now iterating at: 17:06:29 rms-change max change #iterations 3.264521 165.8301 at 10iterations 1.361827 57.24282 at 20iterations 0.5720720 22.46642 at 30iterations 0.2407798 10.19593 at 40iterations 0.1012817 4.208935 at 50iterations 4.2631824E-02 1.585209 at 60iterations 1.7937852E-02 0.7018552 at 70iterations 7.5417710E-03 0.2729769 at 80iterations 3.1870129E-03 0.1425066 at 90iterations 1.3414426E-03 5.1208496E-02 at 100iterations 5.6521985E-04 2.1500587E-02 at 110iterations 2.3839812E-04 8.3818436E-03 at 120iterations finished qdiffx linear iterations at : 17:06:36 total time elapsed so far: 8.520000 # loops : 120 mean,max change (kT/e) : 2.3839812E-04 8.3818436E-03 energy calculations done at 8.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.680000 DelPhi exited at 17:06:37 8.689u 0.453s 0:09.52 95.9% 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 Mon Oct 10 2011 at 17:06:37 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2682 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: 2.494278 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): -40.49500 6.727000 ymin,ymax (A): -9.829000 41.69500 zmin,zma (A): -61.76200 2.465000 x,y,z range (A): 47.22200 51.52400 64.22701 scale (grids/A): 2.494278 object centre (A): -16.88400 15.93300 -29.64850 number of atom coordinates read : 2682 total number of charged atoms : 2543 net assigned charge : 6.000023 assigned positive charge : 403.2636 centred at (gu) : 88.58430 88.65498 92.65931 assigned negative charge : -397.2646 centred at (gu) : 88.46132 88.23852 92.37766 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 138140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25892 grid for indexing accessible points = 1.400000 m= 60837 mr = 95153 m= 16411 mr = 46652 m= 2546 mr = 11710 m= 166 mr = 1569 m= 4 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 62988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 20327 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) : 1.662852 object centre at (A) : -16.88400 15.93300 -29.64850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5904455 0.2266868 midg,1,midg; midg,igrid,midg -0.1117605 4.5334692E-03 1,midg,midg; igrid,midg,midg -4.0417672E-03 9.0452693E-02 gauss-seidel spectral radius is 0.9991494 estimated iterations to convergence 271 setup time was (sec) 1.490000 now iterating at: 17:06:39 rms-change max change #iterations 8.546797 343.4576 at 10iterations 4.867234 120.8756 at 20iterations 2.735710 70.96561 at 30iterations 1.530535 37.03876 at 40iterations 0.8513478 19.43276 at 50iterations 0.4729839 10.55915 at 60iterations 0.2611392 5.967017 at 70iterations 0.1444027 3.533801 at 80iterations 7.9854533E-02 1.901766 at 90iterations 4.4133123E-02 0.9524372 at 100iterations 2.4348844E-02 0.5330105 at 110iterations 1.3434129E-02 0.2886600 at 120iterations 7.3970417E-03 0.1727715 at 130iterations 4.0695705E-03 9.3112946E-02 at 140iterations 2.2475317E-03 4.6935558E-02 at 150iterations 1.2370815E-03 2.6725888E-02 at 160iterations 6.8188226E-04 1.6738892E-02 at 170iterations 3.7661270E-04 8.8720322E-03 at 180iterations finished qdiffx linear iterations at : 17:06:52 total time elapsed so far: 14.51000 # loops : 180 mean,max change (kT/e) : 3.7661270E-04 8.8720322E-03 energy calculations done at 14.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.69000 DelPhi exited at 17:06:53 14.692u 0.424s 0:15.51 97.4% 0+0k 0+0io 0pf+0w