Sun Oct 9 19:55:13 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 19:55:13 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 = 5391 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4994459 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): 3.290000 68.24000 ymin,ymax (A): -8.681000 53.56600 zmin,zma (A): -2.390000 68.88900 x,y,z range (A): 64.95000 62.24700 71.27900 scale (grids/A): 0.4994459 object centre (A): 35.76500 22.44250 33.24950 number of atom coordinates read : 5391 total number of charged atoms : 5235 net assigned charge : 4.740026 assigned positive charge : 828.1002 centred at (gu) : 88.35282 89.25883 88.75911 assigned negative charge : -823.3661 centred at (gu) : 88.29386 89.29179 88.69164 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8583 nv = 96 ne = 84 npr = 108630 no. pairs analyzed = 108630 no. exposed pairs = 6262 no. arc points = 42727 no. surface atoms = 2131 nbur = 3260 mkacc time = 0.2600000 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 = 1.736000 m= 298 mr = 4763 m= 0 mr = 5 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4201 ## 604 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11511 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1453849E-10 1.1862007E-10 midg,1,midg; midg,igrid,midg 1.2619493E-10 -1.3572861E-11 1,midg,midg; igrid,midg,midg -1.0364576E-10 9.6706150E-11 gauss-seidel spectral radius is 0.9795398 estimated iterations to convergence 58 setup time was (sec) 0.7600000 now iterating at: 19:55:14 rms-change max change #iterations 7.0835285E-02 9.885584 at 10iterations 9.7715324E-03 1.596478 at 20iterations 4.0088221E-03 0.7351151 at 30iterations 1.8143849E-03 0.3305435 at 40iterations 8.3161297E-04 0.1485596 at 50iterations finished qdiffx linear iterations at : 19:55:16 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 8.3161297E-04 0.1485596 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 19:55:17 3.591u 0.153s 0:04.06 92.1% 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 Sun Oct 9 2011 at 19:55:17 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 = 5391 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.498338 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): 3.290000 68.24000 ymin,ymax (A): -8.681000 53.56600 zmin,zma (A): -2.390000 68.88900 x,y,z range (A): 64.95000 62.24700 71.27900 scale (grids/A): 1.498338 object centre (A): 35.76500 22.44250 33.24950 number of atom coordinates read : 5391 total number of charged atoms : 5235 net assigned charge : 4.740026 assigned positive charge : 828.1002 centred at (gu) : 85.05719 87.77545 86.27531 assigned negative charge : -823.3661 centred at (gu) : 84.88139 87.87511 86.07487 start vw surface at 0.2300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 98438 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42727 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 30045 mr = 70874 m= 2496 mr = 20786 m= 39 mr = 1039 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 38319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 569 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 39011 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) : 0.4994459 object centre at (A) : 35.76500 22.44250 33.24950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0073444E-02 1.4471659E-02 midg,1,midg; midg,igrid,midg 1.1218282E-02 3.9396761E-03 1,midg,midg; igrid,midg,midg -8.3227670E-03 3.2930175E-04 gauss-seidel spectral radius is 0.9980574 estimated iterations to convergence 180 setup time was (sec) 1.020000 now iterating at: 19:55:18 rms-change max change #iterations 3.899463 154.4855 at 10iterations 1.581414 64.22308 at 20iterations 0.6406108 21.12074 at 30iterations 0.2609878 8.371101 at 40iterations 0.1069461 3.502319 at 50iterations 4.4865876E-02 1.373405 at 60iterations 2.0036420E-02 0.6267853 at 70iterations 1.0268085E-02 0.3453932 at 80iterations 6.2757530E-03 0.2312927 at 90iterations 4.2858776E-03 0.1484756 at 100iterations 3.1138058E-03 0.1039963 at 110iterations 2.3010543E-03 7.6042175E-02 at 120iterations finished qdiffx linear iterations at : 19:55:25 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 2.3010543E-03 7.6042175E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 19:55:25 7.786u 0.149s 0:08.21 96.4% 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 Sun Oct 9 2011 at 19:55:25 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 = 5391 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.247506 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): 3.290000 68.24000 ymin,ymax (A): -8.681000 53.56600 zmin,zma (A): -2.390000 68.88900 x,y,z range (A): 64.95000 62.24700 71.27900 scale (grids/A): 2.247506 object centre (A): 35.76500 22.44250 33.24950 number of atom coordinates read : 5391 total number of charged atoms : 5235 net assigned charge : 4.740026 assigned positive charge : 828.1002 centred at (gu) : 82.58536 86.66275 84.41261 assigned negative charge : -823.3661 centred at (gu) : 82.32207 86.81262 84.11234 start vw surface at 0.2300000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 229673 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42727 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 107818 mr = 173298 m= 27866 mr = 86497 m= 3551 mr = 20576 m= 157 mr = 2077 m= 0 mr = 61 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.750000 number of dielectric boundary points 86556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 41679 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) : 1.498338 object centre at (A) : 35.76500 22.44250 33.24950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2925330 0.5654578 midg,1,midg; midg,igrid,midg 0.2105915 4.5050222E-02 1,midg,midg; igrid,midg,midg -0.2391063 -4.7659152E-03 gauss-seidel spectral radius is 0.9991458 estimated iterations to convergence 270 setup time was (sec) 2.050000 now iterating at: 19:55:28 rms-change max change #iterations 10.56178 284.7631 at 10iterations 5.982911 131.2864 at 20iterations 3.355103 66.69433 at 30iterations 1.876651 36.35446 at 40iterations 1.045316 20.57363 at 50iterations 0.5826513 11.28433 at 60iterations 0.3227800 7.208368 at 70iterations 0.1794735 3.160801 at 80iterations 9.9696793E-02 1.938748 at 90iterations 5.5515055E-02 1.002470 at 100iterations 3.1203084E-02 0.5590591 at 110iterations 1.7830711E-02 0.3390808 at 120iterations 1.0532963E-02 0.2304668 at 130iterations 6.5577780E-03 0.1435318 at 140iterations 4.3876371E-03 9.6427917E-02 at 150iterations 3.1687757E-03 6.5986633E-02 at 160iterations 2.4276273E-03 4.9057007E-02 at 170iterations 1.9229775E-03 3.8681030E-02 at 180iterations finished qdiffx linear iterations at : 19:55:39 total time elapsed so far: 13.39000 # loops : 180 mean,max change (kT/e) : 1.9229775E-03 3.8681030E-02 energy calculations done at 13.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.59000 DelPhi exited at 19:55:39 13.596u 0.173s 0:14.04 98.0% 0+0k 0+0io 0pf+0w