Sat Oct 8 17:32:36 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 8 2011 at 17:32:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3547 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 0.5244550 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): -1.320000 44.56100 ymin,ymax (A): -30.42900 25.94400 zmin,zma (A): 1.593000 69.47300 x,y,z range (A): 45.88100 56.37300 67.88000 scale (grids/A): 0.5244550 object centre (A): 21.62050 -2.242499 35.53300 number of atom coordinates read : 3547 total number of charged atoms : 3400 net assigned charge : -5.771982 assigned positive charge : 537.7720 centred at (gu) : 90.35474 91.66787 90.51688 assigned negative charge : -543.5458 centred at (gu) : 90.31599 91.62747 90.51142 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6156 nv = 96 ne = 84 npr = 72745 no. pairs analyzed = 72745 no. exposed pairs = 4313 no. arc points = 29721 no. surface atoms = 1465 nbur = 2082 mkacc time = 0.1600000 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 = 1.624000 m= 217 mr = 3260 m= 0 mr = 11 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2943 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8191 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5071011E-10 -1.5153302E-10 midg,1,midg; midg,igrid,midg -1.9327588E-10 -1.3453141E-11 1,midg,midg; igrid,midg,midg -2.6388552E-10 -1.8283314E-11 gauss-seidel spectral radius is 0.9813071 estimated iterations to convergence 60 setup time was (sec) 0.5700000 now iterating at: 17:32:37 rms-change max change #iterations 6.4973786E-02 10.12668 at 10iterations 4.1486826E-03 0.7023859 at 20iterations 4.1714407E-04 7.6036453E-02 at 30iterations 9.5823649E-05 1.9737244E-02 at 40iterations 2.6089245E-05 5.2862167E-03 at 50iterations finished qdiffx linear iterations at : 17:32:40 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 2.6089245E-05 5.2862167E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 17:32:40 3.166u 0.142s 0:03.60 91.6% 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 8 2011 at 17:32:40 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 = 3547 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 1.573365 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): -1.320000 44.56100 ymin,ymax (A): -30.42900 25.94400 zmin,zma (A): 1.593000 69.47300 x,y,z range (A): 45.88100 56.37300 67.88000 scale (grids/A): 1.573365 object centre (A): 21.62050 -2.242499 35.53300 number of atom coordinates read : 3547 total number of charged atoms : 3400 net assigned charge : -5.771982 assigned positive charge : 537.7720 centred at (gu) : 91.06313 95.00259 91.54986 assigned negative charge : -543.5458 centred at (gu) : 90.94771 94.88190 91.53389 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29721 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20739 mr = 47948 m= 1950 mr = 14250 m= 50 mr = 880 m= 0 mr = 4 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 28811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 425 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 25759 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) : 0.5244550 object centre at (A) : 21.62050 -2.242499 35.53300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6955429E-03 1.3180993E-02 midg,1,midg; midg,igrid,midg -8.4188506E-03 -1.0914764E-02 1,midg,midg; igrid,midg,midg -4.0008374E-03 8.6103001E-04 gauss-seidel spectral radius is 0.9980822 estimated iterations to convergence 181 setup time was (sec) 0.7800000 now iterating at: 17:32:41 rms-change max change #iterations 3.368122 149.7359 at 10iterations 1.366445 52.81508 at 20iterations 0.5560437 20.03241 at 30iterations 0.2276240 7.982889 at 40iterations 9.2760779E-02 3.629089 at 50iterations 3.7795641E-02 1.433789 at 60iterations 1.5383216E-02 0.5896616 at 70iterations 6.3256323E-03 0.2227688 at 80iterations 2.6054208E-03 9.7860336E-02 at 90iterations 1.0957005E-03 3.8898468E-02 at 100iterations 4.7676751E-04 1.7288208E-02 at 110iterations 2.2181140E-04 8.3618164E-03 at 120iterations finished qdiffx linear iterations at : 17:32:47 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 2.2181140E-04 8.3618164E-03 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 17:32:48 7.068u 0.225s 0:07.57 96.1% 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 8 2011 at 17:32:48 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 = 3547 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 2.360047 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): -1.320000 44.56100 ymin,ymax (A): -30.42900 25.94400 zmin,zma (A): 1.593000 69.47300 x,y,z range (A): 45.88100 56.37300 67.88000 scale (grids/A): 2.360047 object centre (A): 21.62050 -2.242499 35.53300 number of atom coordinates read : 3547 total number of charged atoms : 3400 net assigned charge : -5.771982 assigned positive charge : 537.7720 centred at (gu) : 91.59464 97.50355 92.32426 assigned negative charge : -543.5458 centred at (gu) : 91.42139 97.32267 92.30083 start vw surface at 0.1700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 160667 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29721 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73910 mr = 117295 m= 19711 mr = 58483 m= 2788 mr = 14560 m= 158 mr = 1734 m= 2 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.200000 number of dielectric boundary points 65101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 27142 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) : 1.573365 object centre at (A) : 21.62050 -2.242499 35.53300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2846229 0.1650668 midg,1,midg; midg,igrid,midg -0.1166836 -0.1570525 1,midg,midg; igrid,midg,midg -6.6709839E-02 4.1704822E-02 gauss-seidel spectral radius is 0.9991114 estimated iterations to convergence 265 setup time was (sec) 1.510000 now iterating at: 17:32:49 rms-change max change #iterations 8.906033 243.3297 at 10iterations 4.935025 109.4660 at 20iterations 2.730394 65.93666 at 30iterations 1.499768 31.30609 at 40iterations 0.8226941 17.84897 at 50iterations 0.4484813 9.509800 at 60iterations 0.2455730 4.894346 at 70iterations 0.1341601 2.620134 at 80iterations 7.3218010E-02 1.623492 at 90iterations 3.9961789E-02 0.8188877 at 100iterations 2.1774130E-02 0.4680634 at 110iterations 1.1868061E-02 0.2395439 at 120iterations 6.4765010E-03 0.1286626 at 130iterations 3.5277945E-03 6.9139481E-02 at 140iterations 1.9336940E-03 3.8818359E-02 at 150iterations 1.0628439E-03 2.1697998E-02 at 160iterations 5.9030054E-04 1.2372494E-02 at 170iterations 3.3215477E-04 7.6141357E-03 at 180iterations finished qdiffx linear iterations at : 17:33:04 total time elapsed so far: 15.68000 # loops : 180 mean,max change (kT/e) : 3.3215477E-04 7.6141357E-03 energy calculations done at 15.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.86000 DelPhi exited at 17:33:04 15.860u 0.261s 0:16.38 98.4% 0+0k 0+0io 0pf+0w