Sun Oct 9 08:53:55 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 Sun Oct 9 2011 at 08:53:55 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 = 5657 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: 0.5134492 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): 8.184999 77.52000 ymin,ymax (A): -13.12100 50.44600 zmin,zma (A): -18.59800 50.66200 x,y,z range (A): 69.33500 63.56700 69.26000 scale (grids/A): 0.5134492 object centre (A): 42.85250 18.66250 16.03200 number of atom coordinates read : 5657 total number of charged atoms : 5489 net assigned charge : -5.999973 assigned positive charge : 849.3668 centred at (gu) : 89.85210 89.45815 88.98502 assigned negative charge : -855.3737 centred at (gu) : 89.77628 89.51527 89.01415 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9600 nv = 96 ne = 84 npr = 113121 no. pairs analyzed = 113121 no. exposed pairs = 7158 no. arc points = 49131 no. surface atoms = 2396 nbur = 3261 mkacc time = 0.2400000 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 = 1.652000 m= 344 mr = 5006 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4835 ## 701 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12731 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8420816E-12 -1.5442420E-10 midg,1,midg; midg,igrid,midg 1.1659969E-10 -2.6043120E-10 1,midg,midg; igrid,midg,midg -3.8140785E-10 1.5815169E-10 gauss-seidel spectral radius is 0.9806666 estimated iterations to convergence 59 setup time was (sec) 0.7400000 now iterating at: 08:53:56 rms-change max change #iterations 7.6086469E-02 9.979474 at 10iterations 4.5348164E-03 0.7226934 at 20iterations 5.1851169E-04 0.1133118 at 30iterations 1.5596551E-04 3.6188126E-02 at 40iterations 5.3850265E-05 1.2102127E-02 at 50iterations finished qdiffx linear iterations at : 08:53:59 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 5.3850265E-05 1.2102127E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 08:53:59 3.532u 0.196s 0:04.05 91.8% 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 Sun Oct 9 2011 at 08:53:59 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 = 5657 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.540348 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): 8.184999 77.52000 ymin,ymax (A): -13.12100 50.44600 zmin,zma (A): -18.59800 50.66200 x,y,z range (A): 69.33500 63.56700 69.26000 scale (grids/A): 1.540348 object centre (A): 42.85250 18.66250 16.03200 number of atom coordinates read : 5657 total number of charged atoms : 5489 net assigned charge : -5.999973 assigned positive charge : 849.3668 centred at (gu) : 89.55468 88.37235 86.95325 assigned negative charge : -855.3737 centred at (gu) : 89.32851 88.54594 87.04211 start vw surface at 0.2200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 108307 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49131 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 32094 mr = 74695 m= 2730 mr = 21324 m= 34 mr = 1144 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1028 time to turn everything in is 0.7700000 number of dielectric boundary points 46002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 674 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 41326 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) : 0.5134492 object centre at (A) : 42.85250 18.66250 16.03200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3139903E-03 -2.1270996E-02 midg,1,midg; midg,igrid,midg 1.2907237E-03 -4.3880502E-03 1,midg,midg; igrid,midg,midg -2.1618433E-02 2.4857917E-03 gauss-seidel spectral radius is 0.9982224 estimated iterations to convergence 188 setup time was (sec) 1.080000 now iterating at: 08:54:01 rms-change max change #iterations 4.250663 155.8485 at 10iterations 1.788233 51.16968 at 20iterations 0.7499858 22.22538 at 30iterations 0.3156911 9.223738 at 40iterations 0.1332700 3.656902 at 50iterations 5.6233022E-02 1.720690 at 60iterations 2.3671200E-02 0.8171215 at 70iterations 1.0016279E-02 0.2682705 at 80iterations 4.2626229E-03 0.1235523 at 90iterations 1.8287757E-03 5.2131653E-02 at 100iterations 8.0240681E-04 2.4702072E-02 at 110iterations 3.7245362E-04 1.4872551E-02 at 120iterations finished qdiffx linear iterations at : 08:54:08 total time elapsed so far: 8.570000 # loops : 120 mean,max change (kT/e) : 3.7245362E-04 1.4872551E-02 energy calculations done at 8.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.730000 DelPhi exited at 08:54:09 8.737u 0.235s 0:09.26 96.7% 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 Sun Oct 9 2011 at 08:54:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5657 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: 2.310521 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): 8.184999 77.52000 ymin,ymax (A): -13.12100 50.44600 zmin,zma (A): -18.59800 50.66200 x,y,z range (A): 69.33500 63.56700 69.26000 scale (grids/A): 2.310521 object centre (A): 42.85250 18.66250 16.03200 number of atom coordinates read : 5657 total number of charged atoms : 5489 net assigned charge : -5.999973 assigned positive charge : 849.3668 centred at (gu) : 89.33170 87.55820 85.42952 assigned negative charge : -855.3737 centred at (gu) : 88.99269 87.81902 85.56303 start vw surface at 0.2200000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 251940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49131 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 114636 mr = 183239 m= 29131 mr = 89520 m= 3946 mr = 20802 m= 214 mr = 2374 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 3295 time to turn everything in is 1.800000 number of dielectric boundary points 103867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 43791 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) : 1.540348 object centre at (A) : 42.85250 18.66250 16.03200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2504972 -0.5248727 midg,1,midg; midg,igrid,midg 5.9853785E-02 -6.5701045E-02 1,midg,midg; igrid,midg,midg -0.6518803 4.1975826E-02 gauss-seidel spectral radius is 0.9992206 estimated iterations to convergence 283 setup time was (sec) 2.140000 now iterating at: 08:54:11 rms-change max change #iterations 11.53549 306.4910 at 10iterations 6.797813 154.8611 at 20iterations 3.973814 90.79008 at 30iterations 2.304490 45.27149 at 40iterations 1.332488 26.21457 at 50iterations 0.7689890 17.00859 at 60iterations 0.4419376 8.618416 at 70iterations 0.2533706 4.917252 at 80iterations 0.1448554 2.643384 at 90iterations 8.2771599E-02 1.627495 at 100iterations 4.7258157E-02 0.9480648 at 110iterations 2.6971204E-02 0.4515991 at 120iterations 1.5383629E-02 0.3023643 at 130iterations 8.7598199E-03 0.1726837 at 140iterations 4.9925661E-03 9.3269348E-02 at 150iterations 2.8432740E-03 5.0018311E-02 at 160iterations 1.6227708E-03 2.9776692E-02 at 170iterations 9.3023223E-04 1.5094757E-02 at 180iterations finished qdiffx linear iterations at : 08:54:22 total time elapsed so far: 13.14000 # loops : 180 mean,max change (kT/e) : 9.3023223E-04 1.5094757E-02 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 08:54:22 13.327u 0.204s 0:13.81 97.9% 0+0k 0+0io 0pf+0w