Sat Oct 15 14:58:28 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+sph.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 Sat Oct 15 2011 at 14:58:28 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6013920 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): -10.21000 40.64300 ymin,ymax (A): 30.49200 89.68800 zmin,zma (A): -10.13700 45.67600 x,y,z range (A): 50.85300 59.19600 55.81300 scale (grids/A): 0.6013920 object centre (A): 15.21650 60.09000 17.76950 number of atom coordinates read : 2710 total number of charged atoms : 2572 net assigned charge : 0.5000073 assigned positive charge : 399.9297 centred at (gu) : 90.57283 89.33605 89.44265 assigned negative charge : -399.4308 centred at (gu) : 90.57731 89.36179 89.46581 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6614 nv = 96 ne = 84 npr = 54260 no. pairs analyzed = 54260 no. exposed pairs = 3894 no. arc points = 27701 no. surface atoms = 1281 nbur = 1429 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 311 mr = 3136 m= 0 mr = 14 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3775 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2738 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8179 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2691772E-09 -6.1317618E-10 midg,1,midg; midg,igrid,midg 1.4178834E-09 -6.8529277E-10 1,midg,midg; igrid,midg,midg 3.4059464E-10 3.9443365E-11 gauss-seidel spectral radius is 0.9857118 estimated iterations to convergence 69 setup time was (sec) 0.3900000 now iterating at: 14:58:28 rms-change max change #iterations 0.1055982 19.37035 at 10iterations 9.1606854E-03 1.326836 at 20iterations 8.2305877E-04 0.1397076 at 30iterations 7.9237187E-05 1.2069702E-02 at 40iterations 9.9575718E-06 1.4896393E-03 at 50iterations finished qdiffx linear iterations at : 14:58:31 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 9.9575718E-06 1.4896393E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:58:32 3.394u 0.169s 0:03.87 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 Sat Oct 15 2011 at 14:58:32 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.804176 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): -10.21000 40.64300 ymin,ymax (A): 30.49200 89.68800 zmin,zma (A): -10.13700 45.67600 x,y,z range (A): 50.85300 59.19600 55.81300 scale (grids/A): 1.804176 object centre (A): 15.21650 60.09000 17.76950 number of atom coordinates read : 2710 total number of charged atoms : 2572 net assigned charge : 0.5000073 assigned positive charge : 399.9297 centred at (gu) : 91.71791 88.00741 88.32714 assigned negative charge : -399.4308 centred at (gu) : 91.73186 88.08513 88.39736 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 70527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27701 grid for indexing accessible points = 1.400000 m= 23354 mr = 45174 m= 3264 mr = 15553 m= 148 mr = 1609 m= 2 mr = 18 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 0.3700000 number of dielectric boundary points 34941 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 20073 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) : 0.6013920 object centre at (A) : 15.21650 60.09000 17.76950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9160667E-03 -1.9930363E-02 midg,1,midg; midg,igrid,midg 2.3836503E-02 -1.8305942E-02 1,midg,midg; igrid,midg,midg 2.2353444E-03 -6.4860348E-04 gauss-seidel spectral radius is 0.9985158 estimated iterations to convergence 206 setup time was (sec) 0.6200000 now iterating at: 14:58:32 rms-change max change #iterations 3.867925 186.5537 at 10iterations 1.730418 65.09064 at 20iterations 0.7835209 30.92527 at 30iterations 0.3540412 11.60211 at 40iterations 0.1596501 5.399231 at 50iterations 7.2030194E-02 2.372736 at 60iterations 3.2750502E-02 1.224409 at 70iterations 1.4760076E-02 0.4880066 at 80iterations 6.7119841E-03 0.2223358 at 90iterations 3.0282363E-03 0.1021309 at 100iterations 1.3674054E-03 5.1812172E-02 at 110iterations 6.2162778E-04 1.9138336E-02 at 120iterations finished qdiffx linear iterations at : 14:58:41 total time elapsed so far: 8.740000 # loops : 120 mean,max change (kT/e) : 6.2162778E-04 1.9138336E-02 energy calculations done at 8.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.880000 DelPhi exited at 14:58:41 8.881u 0.286s 0:09.44 97.0% 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 15 2011 at 14:58:41 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.706264 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): -10.21000 40.64300 ymin,ymax (A): 30.49200 89.68800 zmin,zma (A): -10.13700 45.67600 x,y,z range (A): 50.85300 59.19600 55.81300 scale (grids/A): 2.706264 object centre (A): 15.21650 60.09000 17.76950 number of atom coordinates read : 2710 total number of charged atoms : 2572 net assigned charge : 0.5000073 assigned positive charge : 399.9297 centred at (gu) : 92.57667 87.01104 87.49059 assigned negative charge : -399.4308 centred at (gu) : 92.59782 87.12769 87.59592 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 163598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27701 grid for indexing accessible points = 1.400000 m= 76060 mr = 111502 m= 25950 mr = 58507 m= 5466 mr = 19052 m= 589 mr = 3440 m= 15 mr = 282 m= 1 mr = 3 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 0.9500000 number of dielectric boundary points 78893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 20563 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) : 1.804176 object centre at (A) : 15.21650 60.09000 17.76950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9336173E-02 -0.2749965 midg,1,midg; midg,igrid,midg 0.4119990 -0.1712201 1,midg,midg; igrid,midg,midg 7.3946625E-02 -2.8059293E-02 gauss-seidel spectral radius is 0.9992407 estimated iterations to convergence 286 setup time was (sec) 1.240000 now iterating at: 14:58:43 rms-change max change #iterations 9.604131 348.8299 at 10iterations 5.694946 178.5461 at 20iterations 3.331832 84.41286 at 30iterations 1.936793 49.29850 at 40iterations 1.122771 22.43676 at 50iterations 0.6474069 13.80657 at 60iterations 0.3731751 7.360605 at 70iterations 0.2145642 4.620729 at 80iterations 0.1227227 2.410308 at 90iterations 7.0205837E-02 1.410916 at 100iterations 4.0092465E-02 0.7613115 at 110iterations 2.2976195E-02 0.4915314 at 120iterations 1.3113364E-02 0.2492828 at 130iterations 7.4772523E-03 0.1521120 at 140iterations 4.2785681E-03 7.8112602E-02 at 150iterations 2.4454570E-03 4.5543671E-02 at 160iterations 1.3984885E-03 2.5356293E-02 at 170iterations 8.0092798E-04 1.5487671E-02 at 180iterations finished qdiffx linear iterations at : 14:58:56 total time elapsed so far: 14.54000 # loops : 180 mean,max change (kT/e) : 8.0092798E-04 1.5487671E-02 energy calculations done at 14.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.68000 DelPhi exited at 14:58:56 14.681u 0.274s 0:15.22 98.2% 0+0k 0+0io 0pf+0w