Wed Nov 17 01:01:43 PST 2010 #!/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 Wed Nov 17 2010 at 01:01:43 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2660 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: 0.5565979 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): -11.82900 52.13100 ymin,ymax (A): -14.46500 43.13800 zmin,zma (A): 4.451000 51.60900 x,y,z range (A): 63.96000 57.60300 47.15800 scale (grids/A): 0.5565979 object centre (A): 20.15100 14.33650 28.03000 number of atom coordinates read : 2660 total number of charged atoms : 2556 net assigned charge : 7.000020 assigned positive charge : 384.1298 centred at (gu) : 90.78097 92.03479 90.56180 assigned negative charge : -377.1306 centred at (gu) : 90.33688 92.30182 90.39265 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5451 nv = 96 ne = 84 npr = 53097 no. pairs analyzed = 53097 no. exposed pairs = 3594 no. arc points = 25843 no. surface atoms = 1199 nbur = 1461 mkacc time = 9.9999994E-02 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 = 1.540000 m= 264 mr = 2568 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2000000 number of dielectric boundary points 3130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2564 ## 275 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6964 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.5198019E-10 2.3450228E-09 midg,1,midg; midg,igrid,midg 1.7199052E-09 -2.7064246E-09 1,midg,midg; igrid,midg,midg -2.6387985E-09 5.0322173E-09 gauss-seidel spectral radius is 0.9833366 estimated iterations to convergence 64 setup time was (sec) 0.3800000 now iterating at: 01:01:44 rms-change max change #iterations 7.1460776E-02 12.63468 at 10iterations 5.3580077E-03 0.9807043 at 20iterations 5.5318850E-04 0.1147766 at 30iterations 1.0124323E-04 2.4414063E-02 at 40iterations 2.2300437E-05 5.3558350E-03 at 50iterations finished qdiffx linear iterations at : 01:01:47 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.2300437E-05 5.3558350E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 01:01:47 3.362u 0.191s 0:03.84 92.4% 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 Wed Nov 17 2010 at 01:01:47 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2660 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: 1.669794 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): -11.82900 52.13100 ymin,ymax (A): -14.46500 43.13800 zmin,zma (A): 4.451000 51.60900 x,y,z range (A): 63.96000 57.60300 47.15800 scale (grids/A): 1.669794 object centre (A): 20.15100 14.33650 28.03000 number of atom coordinates read : 2660 total number of charged atoms : 2556 net assigned charge : 7.000020 assigned positive charge : 384.1298 centred at (gu) : 92.34263 96.10369 91.68488 assigned negative charge : -377.1306 centred at (gu) : 91.01055 96.90523 91.17785 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25843 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18557 mr = 37535 m= 2449 mr = 12386 m= 82 mr = 1262 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 235 time to turn everything in is 0.3000000 number of dielectric boundary points 29173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 19686 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) : 0.5565979 object centre at (A) : 20.15100 14.33650 28.03000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1372214E-03 1.0055230E-02 midg,1,midg; midg,igrid,midg 1.9530280E-02 -2.7652881E-03 1,midg,midg; igrid,midg,midg -1.5527320E-02 2.5693676E-02 gauss-seidel spectral radius is 0.9982329 estimated iterations to convergence 189 setup time was (sec) 0.5100000 now iterating at: 01:01:48 rms-change max change #iterations 3.156226 173.0993 at 10iterations 1.322855 52.53804 at 20iterations 0.5585967 22.52717 at 30iterations 0.2344629 9.308983 at 40iterations 9.9098384E-02 4.064110 at 50iterations 4.1955978E-02 1.499500 at 60iterations 1.7723197E-02 0.6910553 at 70iterations 7.5525763E-03 0.2855301 at 80iterations 3.2648051E-03 0.1370583 at 90iterations 1.4625766E-03 6.6529751E-02 at 100iterations 6.8421871E-04 3.1011581E-02 at 110iterations 3.4462582E-04 1.6162872E-02 at 120iterations finished qdiffx linear iterations at : 01:01:55 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 3.4462582E-04 1.6162872E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 01:01:55 7.572u 0.228s 0:08.10 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 Wed Nov 17 2010 at 01:01:55 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2660 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: 2.504690 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): -11.82900 52.13100 ymin,ymax (A): -14.46500 43.13800 zmin,zma (A): 4.451000 51.60900 x,y,z range (A): 63.96000 57.60300 47.15800 scale (grids/A): 2.504690 object centre (A): 20.15100 14.33650 28.03000 number of atom coordinates read : 2660 total number of charged atoms : 2556 net assigned charge : 7.000020 assigned positive charge : 384.1298 centred at (gu) : 93.51379 99.15537 92.52729 assigned negative charge : -377.1306 centred at (gu) : 91.51583 100.3579 91.76667 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 137505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25843 grid for indexing accessible points = 1.400000 m= 60925 mr = 92439 m= 19969 mr = 46658 m= 3930 mr = 14934 m= 342 mr = 2640 m= 3 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 819 time to turn everything in is 0.7300000 number of dielectric boundary points 65840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 20436 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) : 1.669794 object centre at (A) : 20.15100 14.33650 28.03000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2855988E-02 9.8997645E-02 midg,1,midg; midg,igrid,midg 0.2144300 -5.6543794E-02 1,midg,midg; igrid,midg,midg -3.4627527E-02 9.0265647E-02 gauss-seidel spectral radius is 0.9991379 estimated iterations to convergence 269 setup time was (sec) 0.9600000 now iterating at: 01:01:56 rms-change max change #iterations 7.949873 339.7188 at 10iterations 4.420524 111.1491 at 20iterations 2.438322 53.47350 at 30iterations 1.344937 34.27287 at 40iterations 0.7400283 16.45841 at 50iterations 0.4069607 9.215137 at 60iterations 0.2236473 5.552541 at 70iterations 0.1230375 2.852347 at 80iterations 6.7528903E-02 1.506760 at 90iterations 3.7036054E-02 0.8059654 at 100iterations 2.0367548E-02 0.4084663 at 110iterations 1.1182076E-02 0.2638474 at 120iterations 6.1640213E-03 0.1548576 at 130iterations 3.3999039E-03 7.2238922E-02 at 140iterations 1.8861485E-03 4.2068481E-02 at 150iterations 1.0568439E-03 2.3305893E-02 at 160iterations 6.0184085E-04 1.4345169E-02 at 170iterations 3.5198967E-04 8.8615417E-03 at 180iterations finished qdiffx linear iterations at : 01:02:07 total time elapsed so far: 11.90000 # loops : 180 mean,max change (kT/e) : 3.5198967E-04 8.8615417E-03 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 01:02:08 12.036u 0.201s 0:12.52 97.6% 0+0k 0+0io 0pf+0w