Sat Oct 15 12:43:47 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 12:43:47 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 = 5661 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5104528 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): 8.287999 77.77900 ymin,ymax (A): -30.69000 33.08800 zmin,zma (A): -19.33300 50.40900 x,y,z range (A): 69.49100 63.77800 69.74200 scale (grids/A): 0.5104528 object centre (A): 43.03350 1.199000 15.53800 number of atom coordinates read : 5661 total number of charged atoms : 5493 net assigned charge : -3.499984 assigned positive charge : 851.1385 centred at (gu) : 89.81706 89.50777 89.24615 assigned negative charge : -854.6457 centred at (gu) : 89.75423 89.57778 89.29031 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 9382 nv = 96 ne = 84 npr = 113625 no. pairs analyzed = 113625 no. exposed pairs = 7185 no. arc points = 49491 no. surface atoms = 2406 nbur = 3255 mkacc time = 0.2000000 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 = 1.680000 m= 331 mr = 4852 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 0.3800000 number of dielectric boundary points 4859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4824 ## 685 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 12547 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0367449E-10 -1.5431083E-10 midg,1,midg; midg,igrid,midg 1.8609275E-10 -2.3630575E-10 1,midg,midg; igrid,midg,midg -2.5898614E-10 1.3420223E-10 gauss-seidel spectral radius is 0.9804381 estimated iterations to convergence 59 setup time was (sec) 0.6500000 now iterating at: 12:43:48 rms-change max change #iterations 7.3659629E-02 11.11772 at 10iterations 4.3356009E-03 0.5765076 at 20iterations 5.1718450E-04 0.1118011 at 30iterations 1.5879609E-04 3.6125183E-02 at 40iterations 5.4776523E-05 1.2035370E-02 at 50iterations finished qdiffx linear iterations at : 12:43:53 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 5.4776523E-05 1.2035370E-02 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 12:43:53 4.040u 0.231s 0:06.50 65.6% 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 12:43:54 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 = 5661 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.531358 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): 8.287999 77.77900 ymin,ymax (A): -30.69000 33.08800 zmin,zma (A): -19.33300 50.40900 x,y,z range (A): 69.49100 63.77800 69.74200 scale (grids/A): 1.531358 object centre (A): 43.03350 1.199000 15.53800 number of atom coordinates read : 5661 total number of charged atoms : 5493 net assigned charge : -3.499984 assigned positive charge : 851.1385 centred at (gu) : 89.44935 88.52137 87.73677 assigned negative charge : -854.6457 centred at (gu) : 89.26228 88.73286 87.87060 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 106621 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49491 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30436 mr = 73285 m= 2525 mr = 19875 m= 38 mr = 943 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 980 time to turn everything in is 0.5500000 number of dielectric boundary points 45517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 684 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 41310 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) : 0.5104528 object centre at (A) : 43.03350 1.199000 15.53800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3919339E-02 -1.9148387E-02 midg,1,midg; midg,igrid,midg 3.3561792E-03 -3.0884326E-03 1,midg,midg; igrid,midg,midg -1.8149296E-02 2.0019514E-03 gauss-seidel spectral radius is 0.9981962 estimated iterations to convergence 187 setup time was (sec) 0.8300000 now iterating at: 12:43:55 rms-change max change #iterations 4.193972 152.1889 at 10iterations 1.748337 56.63507 at 20iterations 0.7306048 21.26048 at 30iterations 0.3066670 8.527203 at 40iterations 0.1280241 3.945122 at 50iterations 5.3776283E-02 1.826942 at 60iterations 2.2498332E-02 0.6520882 at 70iterations 9.4688293E-03 0.2848015 at 80iterations 3.9965622E-03 0.1266232 at 90iterations 1.7172836E-03 5.3793907E-02 at 100iterations 7.5170858E-04 2.4909973E-02 at 110iterations 3.5040008E-04 1.4366150E-02 at 120iterations finished qdiffx linear iterations at : 12:44:06 total time elapsed so far: 9.160000 # loops : 120 mean,max change (kT/e) : 3.5040008E-04 1.4366150E-02 energy calculations done at 9.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.290000 DelPhi exited at 12:44:07 9.294u 0.298s 0:13.54 70.7% 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 12:44:07 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 = 5661 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.297038 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): 8.287999 77.77900 ymin,ymax (A): -30.69000 33.08800 zmin,zma (A): -19.33300 50.40900 x,y,z range (A): 69.49100 63.77800 69.74200 scale (grids/A): 2.297038 object centre (A): 43.03350 1.199000 15.53800 number of atom coordinates read : 5661 total number of charged atoms : 5493 net assigned charge : -3.499984 assigned positive charge : 851.1385 centred at (gu) : 89.17336 87.78182 86.60494 assigned negative charge : -854.6457 centred at (gu) : 88.89327 88.09917 86.80598 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 248593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49491 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 110227 mr = 180251 m= 26860 mr = 85291 m= 3438 mr = 18818 m= 164 mr = 1997 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 3084 time to turn everything in is 1.300000 number of dielectric boundary points 102892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 43803 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) : 1.531358 object centre at (A) : 43.03350 1.199000 15.53800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5141258 -0.5438619 midg,1,midg; midg,igrid,midg 4.6351939E-02 -4.7177419E-02 1,midg,midg; igrid,midg,midg -0.6699998 2.0004679E-02 gauss-seidel spectral radius is 0.9992124 estimated iterations to convergence 281 setup time was (sec) 1.570000 now iterating at: 12:44:09 rms-change max change #iterations 11.34709 362.3717 at 10iterations 6.643620 174.2379 at 20iterations 3.880617 88.42222 at 30iterations 2.242369 49.46960 at 40iterations 1.291938 26.26973 at 50iterations 0.7425520 14.69293 at 60iterations 0.4255327 8.363776 at 70iterations 0.2431725 4.360596 at 80iterations 0.1388030 2.413860 at 90iterations 7.9089120E-02 1.352437 at 100iterations 4.5007233E-02 0.8226089 at 110iterations 2.5633072E-02 0.4622765 at 120iterations 1.4586748E-02 0.2456055 at 130iterations 8.2690269E-03 0.1471934 at 140iterations 4.7041392E-03 7.8147888E-02 at 150iterations 2.6722304E-03 4.7451019E-02 at 160iterations 1.5221289E-03 2.4602890E-02 at 170iterations 8.7154360E-04 1.4970779E-02 at 180iterations finished qdiffx linear iterations at : 12:44:27 total time elapsed so far: 15.20000 # loops : 180 mean,max change (kT/e) : 8.7154360E-04 1.4970779E-02 energy calculations done at 15.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.33000 DelPhi exited at 12:44:28 15.332u 0.300s 0:20.52 76.1% 0+0k 0+0io 0pf+0w