Sat Oct 8 14:54:28 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 14:54:28 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: NAP 318 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5958558 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): 28.01400 87.76000 ymin,ymax (A): 11.98900 68.08500 zmin,zma (A): 70.79200 118.6000 x,y,z range (A): 59.74600 56.09600 47.80800 scale (grids/A): 0.5958558 object centre (A): 57.88700 40.03700 94.69600 number of atom coordinates read : 3040 total number of charged atoms : 2888 net assigned charge : -3.499991 assigned positive charge : 453.7756 centred at (gu) : 89.82734 89.21837 89.82529 assigned negative charge : -457.2762 centred at (gu) : 89.90456 89.30424 89.73685 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6927 nv = 96 ne = 84 npr = 65051 no. pairs analyzed = 65051 no. exposed pairs = 3451 no. arc points = 23570 no. surface atoms = 1176 nbur = 1864 mkacc time = 0.1800000 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 = 1.456000 m= 291 mr = 3966 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2401 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8908 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9013646E-09 1.8944371E-09 midg,1,midg; midg,igrid,midg 2.2721109E-09 -3.8558849E-09 1,midg,midg; igrid,midg,midg 1.6265881E-09 -4.1106518E-09 gauss-seidel spectral radius is 0.9854508 estimated iterations to convergence 68 setup time was (sec) 0.6700000 now iterating at: 14:54:29 rms-change max change #iterations 0.1177328 17.77999 at 10iterations 1.0254593E-02 1.636433 at 20iterations 9.2854409E-04 0.1345978 at 30iterations 1.0365182E-04 1.5442848E-02 at 40iterations 1.6844826E-05 2.9315948E-03 at 50iterations finished qdiffx linear iterations at : 14:54:32 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 1.6844826E-05 2.9315948E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 14:54:33 4.166u 0.264s 0:04.73 93.4% 0+0k 0+0io 6pf+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 14:54:33 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: NAP 318 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.787567 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): 28.01400 87.76000 ymin,ymax (A): 11.98900 68.08500 zmin,zma (A): 70.79200 118.6000 x,y,z range (A): 59.74600 56.09600 47.80800 scale (grids/A): 1.787567 object centre (A): 57.88700 40.03700 94.69600 number of atom coordinates read : 3040 total number of charged atoms : 2888 net assigned charge : -3.499991 assigned positive charge : 453.7756 centred at (gu) : 89.48160 87.65443 89.47488 assigned negative charge : -457.2762 centred at (gu) : 89.71355 87.91272 89.21029 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23570 grid for indexing accessible points = 1.400000 m= 25685 mr = 55001 m= 3120 mr = 18991 m= 125 mr = 1730 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 191 time to turn everything in is 0.6700000 number of dielectric boundary points 29800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 22504 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) : 0.5958558 object centre at (A) : 57.88700 40.03700 94.69600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6128145E-03 7.3529230E-03 midg,1,midg; midg,igrid,midg -1.6464870E-02 -2.3859449E-02 1,midg,midg; igrid,midg,midg 8.6811595E-03 -2.8467333E-02 gauss-seidel spectral radius is 0.9984906 estimated iterations to convergence 204 setup time was (sec) 0.9800000 now iterating at: 14:54:34 rms-change max change #iterations 4.138104 187.3376 at 10iterations 1.855063 62.34364 at 20iterations 0.8385115 28.67154 at 30iterations 0.3801159 12.21585 at 40iterations 0.1704444 5.902023 at 50iterations 7.7060662E-02 2.425129 at 60iterations 3.4855396E-02 1.088209 at 70iterations 1.5791118E-02 0.4808359 at 80iterations 7.0956550E-03 0.2416315 at 90iterations 3.1963701E-03 9.4935417E-02 at 100iterations 1.4518395E-03 4.4065833E-02 at 110iterations 6.5401581E-04 2.1881104E-02 at 120iterations finished qdiffx linear iterations at : 14:54:42 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 6.5401581E-04 2.1881104E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 14:54:43 9.553u 0.291s 0:10.13 97.1% 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 14:54:43 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: NAP 318 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.681351 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): 28.01400 87.76000 ymin,ymax (A): 11.98900 68.08500 zmin,zma (A): 70.79200 118.6000 x,y,z range (A): 59.74600 56.09600 47.80800 scale (grids/A): 2.681351 object centre (A): 57.88700 40.03700 94.69600 number of atom coordinates read : 3040 total number of charged atoms : 2888 net assigned charge : -3.499991 assigned positive charge : 453.7756 centred at (gu) : 89.22223 86.48141 89.21225 assigned negative charge : -457.2762 centred at (gu) : 89.57014 86.86896 88.81551 start vw surface at 0.1600000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 178050 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23570 grid for indexing accessible points = 1.400000 m= 86748 mr = 133651 m= 27522 mr = 71390 m= 5157 mr = 21810 m= 526 mr = 3601 m= 18 mr = 305 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 610 time to turn everything in is 1.670000 number of dielectric boundary points 67264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 23101 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) : 1.787567 object centre at (A) : 57.88700 40.03700 94.69600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3035992E-02 6.3857920E-02 midg,1,midg; midg,igrid,midg -0.2482018 -0.2508769 1,midg,midg; igrid,midg,midg 0.1049655 -0.2584622 gauss-seidel spectral radius is 0.9992180 estimated iterations to convergence 282 setup time was (sec) 1.990000 now iterating at: 14:54:45 rms-change max change #iterations 9.833751 271.9159 at 10iterations 5.671028 175.5320 at 20iterations 3.231622 68.24342 at 30iterations 1.842116 39.01550 at 40iterations 1.048320 20.65751 at 50iterations 0.5963032 10.69576 at 60iterations 0.3382218 6.025306 at 70iterations 0.1912274 3.464512 at 80iterations 0.1085490 2.061371 at 90iterations 6.1470456E-02 1.123079 at 100iterations 3.4899015E-02 0.7241726 at 110iterations 1.9779684E-02 0.3531895 at 120iterations 1.1167218E-02 0.2095699 at 130iterations 6.3405656E-03 0.1145077 at 140iterations 3.5878534E-03 6.9969177E-02 at 150iterations 2.0311244E-03 3.9262533E-02 at 160iterations 1.1495840E-03 2.0521164E-02 at 170iterations 6.5272872E-04 1.2405396E-02 at 180iterations finished qdiffx linear iterations at : 14:54:59 total time elapsed so far: 15.76000 # loops : 180 mean,max change (kT/e) : 6.5272872E-04 1.2405396E-02 energy calculations done at 15.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.95000 DelPhi exited at 14:55:00 15.950u 0.348s 0:16.59 98.1% 0+0k 0+0io 0pf+0w