Mon Oct 10 14:01:40 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 Mon Oct 10 2011 at 14:01:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2855 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6556531 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): -5.313000 44.80800 ymin,ymax (A): 6.114000 60.41100 zmin,zma (A): -10.11600 43.96100 x,y,z range (A): 50.12100 54.29700 54.07700 scale (grids/A): 0.6556531 object centre (A): 19.74750 33.26250 16.92250 number of atom coordinates read : 2855 total number of charged atoms : 2767 net assigned charge : -4.499964 assigned positive charge : 422.3180 centred at (gu) : 90.96306 91.44180 89.26689 assigned negative charge : -426.8198 centred at (gu) : 90.92297 91.47787 89.18817 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8790 nv = 96 ne = 84 npr = 54803 no. pairs analyzed = 54803 no. exposed pairs = 4020 no. arc points = 28360 no. surface atoms = 1329 nbur = 1526 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 613 mr = 4626 m= 4 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2523 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 10045 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9568726E-08 4.3425898E-09 midg,1,midg; midg,igrid,midg -2.3390334E-09 -2.2938863E-08 1,midg,midg; igrid,midg,midg -1.4576498E-08 -2.6000515E-09 gauss-seidel spectral radius is 0.9879884 estimated iterations to convergence 75 setup time was (sec) 0.4300000 now iterating at: 14:01:40 rms-change max change #iterations 0.1723698 25.64140 at 10iterations 1.8265100E-02 2.559158 at 20iterations 1.9309673E-03 0.2887430 at 30iterations 2.5501204E-04 3.7370682E-02 at 40iterations 6.4344858E-05 1.2119293E-02 at 50iterations finished qdiffx linear iterations at : 14:01:43 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 6.4344858E-05 1.2119293E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 14:01:45 3.408u 0.158s 0:05.04 70.4% 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 14:01:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2855 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.966959 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): -5.313000 44.80800 ymin,ymax (A): 6.114000 60.41100 zmin,zma (A): -10.11600 43.96100 x,y,z range (A): 50.12100 54.29700 54.07700 scale (grids/A): 1.966959 object centre (A): 19.74750 33.26250 16.92250 number of atom coordinates read : 2855 total number of charged atoms : 2767 net assigned charge : -4.499964 assigned positive charge : 422.3180 centred at (gu) : 92.88821 94.32450 87.79979 assigned negative charge : -426.8198 centred at (gu) : 92.76872 94.43381 87.56432 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 93372 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28360 grid for indexing accessible points = 1.400000 m= 35720 mr = 62936 m= 7089 mr = 25819 m= 575 mr = 4581 m= 9 mr = 210 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 198 time to turn everything in is 0.4500000 number of dielectric boundary points 43219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 21886 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) : 0.6556531 object centre at (A) : 19.74750 33.26250 16.92250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2160588E-02 -2.1063637E-02 midg,1,midg; midg,igrid,midg 1.6709360E-03 -3.7071686E-02 1,midg,midg; igrid,midg,midg -1.4864739E-02 1.9993929E-02 gauss-seidel spectral radius is 0.9987713 estimated iterations to convergence 226 setup time was (sec) 0.6600000 now iterating at: 14:01:46 rms-change max change #iterations 4.754132 210.6524 at 10iterations 2.312070 73.94247 at 20iterations 1.121937 34.95661 at 30iterations 0.5466420 16.75664 at 40iterations 0.2656904 8.501591 at 50iterations 0.1293609 3.889604 at 60iterations 6.2843151E-02 1.873280 at 70iterations 3.0669121E-02 0.9036021 at 80iterations 1.4931162E-02 0.4464100 at 90iterations 7.2841826E-03 0.2017422 at 100iterations 3.5550690E-03 0.1013870 at 110iterations 1.7363788E-03 4.7302246E-02 at 120iterations finished qdiffx linear iterations at : 14:01:53 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 1.7363788E-03 4.7302246E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 14:01:54 7.850u 0.204s 0:08.95 89.9% 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 14:01:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2855 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.950439 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): -5.313000 44.80800 ymin,ymax (A): 6.114000 60.41100 zmin,zma (A): -10.11600 43.96100 x,y,z range (A): 50.12100 54.29700 54.07700 scale (grids/A): 2.950439 object centre (A): 19.74750 33.26250 16.92250 number of atom coordinates read : 2855 total number of charged atoms : 2767 net assigned charge : -4.499964 assigned positive charge : 422.3180 centred at (gu) : 94.33205 96.48650 86.69945 assigned negative charge : -426.8198 centred at (gu) : 94.15305 96.65062 86.34647 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 215492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28360 grid for indexing accessible points = 1.400000 m= 110885 mr = 153116 m= 45412 mr = 89120 m= 13427 mr = 36223 m= 2388 mr = 10203 m= 181 mr = 1574 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.7099999 no. cavity mid-points inaccessible to solvent = 540 time to turn everything in is 1.200000 number of dielectric boundary points 97479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 22134 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) : 1.966959 object centre at (A) : 19.74750 33.26250 16.92250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9421894E-02 -6.8565674E-02 midg,1,midg; midg,igrid,midg 6.6320688E-02 -0.5903355 1,midg,midg; igrid,midg,midg -0.1924807 0.2453641 gauss-seidel spectral radius is 0.9993145 estimated iterations to convergence 301 setup time was (sec) 1.450000 now iterating at: 14:01:56 rms-change max change #iterations 11.09186 429.0623 at 10iterations 6.644109 143.5074 at 20iterations 3.947968 80.57552 at 30iterations 2.351693 49.34781 at 40iterations 1.390699 25.33803 at 50iterations 0.8231415 14.08332 at 60iterations 0.4852808 8.275642 at 70iterations 0.2864587 4.588840 at 80iterations 0.1686651 2.666651 at 90iterations 9.9341482E-02 1.699020 at 100iterations 5.8378074E-02 0.9063969 at 110iterations 3.4320228E-02 0.6142302 at 120iterations 2.0145146E-02 0.3546641 at 130iterations 1.1841645E-02 0.2178650 at 140iterations 6.9718636E-03 0.1082993 at 150iterations 4.0879590E-03 7.4832916E-02 at 160iterations 2.4092558E-03 3.9184570E-02 at 170iterations 1.4170669E-03 2.4977207E-02 at 180iterations finished qdiffx linear iterations at : 14:02:07 total time elapsed so far: 12.97000 # loops : 180 mean,max change (kT/e) : 1.4170669E-03 2.4977207E-02 energy calculations done at 12.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 14:02:08 13.102u 0.201s 0:13.82 96.2% 0+0k 0+0io 0pf+0w