Sat Oct 8 14:55:00 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+sph2.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 = amb2.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 14:55:00 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! 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 : -3.485991 assigned positive charge : 455.4176 centred at (gu) : 89.84538 89.22522 89.81518 assigned negative charge : -458.9042 centred at (gu) : 89.92218 89.31065 89.72797 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 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 = 0.2100000 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 -4.8691131E-09 1.8634920E-09 midg,1,midg; midg,igrid,midg 2.2695197E-09 -3.8518317E-09 1,midg,midg; igrid,midg,midg 1.6206823E-09 -4.1160120E-09 gauss-seidel spectral radius is 0.9854508 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 14:55:01 rms-change max change #iterations 0.1183543 17.77999 at 10iterations 1.0285494E-02 1.642906 at 20iterations 9.2950143E-04 0.1360130 at 30iterations 1.0315280E-04 1.5225410E-02 at 40iterations 1.6622267E-05 2.8896332E-03 at 50iterations finished qdiffx linear iterations at : 14:55:04 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.6622267E-05 2.8896332E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 14:55:05 4.180u 0.251s 0:04.72 93.8% 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 14:55:05 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! 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 : -3.485991 assigned positive charge : 455.4176 centred at (gu) : 89.53574 87.67499 89.44456 assigned negative charge : -458.9042 centred at (gu) : 89.76639 87.93192 89.18363 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 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 1.8475029E-03 7.3160124E-03 midg,1,midg; midg,igrid,midg -1.6501855E-02 -2.3877170E-02 1,midg,midg; igrid,midg,midg 8.6746179E-03 -2.8597908E-02 gauss-seidel spectral radius is 0.9984906 estimated iterations to convergence 204 setup time was (sec) 0.9700000 now iterating at: 14:55:06 rms-change max change #iterations 4.155638 187.3376 at 10iterations 1.863080 61.39752 at 20iterations 0.8422405 28.67213 at 30iterations 0.3816460 12.30498 at 40iterations 0.1711762 5.951421 at 50iterations 7.7392228E-02 2.428008 at 60iterations 3.4999281E-02 1.089008 at 70iterations 1.5855849E-02 0.4770794 at 80iterations 7.1265614E-03 0.2370291 at 90iterations 3.2101567E-03 9.7432137E-02 at 100iterations 1.4579064E-03 4.4410229E-02 at 110iterations 6.5677951E-04 2.1667480E-02 at 120iterations finished qdiffx linear iterations at : 14:55:14 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 6.5677951E-04 2.1667480E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 14:55:15 9.537u 0.305s 0:10.20 96.3% 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 14:55:15 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! 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 : -3.485991 assigned positive charge : 455.4176 centred at (gu) : 89.30341 86.51222 89.16678 assigned negative charge : -458.9042 centred at (gu) : 89.64940 86.89773 88.77553 start vw surface at 0.1700000 fill in re-entrant regions at 0.5900000 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 = 0.9999999 no. cavity mid-points inaccessible to solvent = 610 time to turn everything in is 1.700000 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 1.860000 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 2.6263310E-02 6.3451879E-02 midg,1,midg; midg,igrid,midg -0.2488018 -0.2510689 1,midg,midg; igrid,midg,midg 0.1048316 -0.2618844 gauss-seidel spectral radius is 0.9992180 estimated iterations to convergence 282 setup time was (sec) 2.030000 now iterating at: 14:55:17 rms-change max change #iterations 9.872833 271.9158 at 10iterations 5.693060 175.5068 at 20iterations 3.243874 68.24294 at 30iterations 1.849045 39.03808 at 40iterations 1.052113 20.62188 at 50iterations 0.5984006 10.58385 at 60iterations 0.3393626 5.998530 at 70iterations 0.1918800 3.458577 at 80iterations 0.1088893 2.071160 at 90iterations 6.1676838E-02 1.137276 at 100iterations 3.5017978E-02 0.7223206 at 110iterations 1.9844176E-02 0.3502827 at 120iterations 1.1203595E-02 0.2097549 at 130iterations 6.3612298E-03 0.1166096 at 140iterations 3.5995340E-03 7.0537567E-02 at 150iterations 2.0376961E-03 3.9382458E-02 at 160iterations 1.1531758E-03 2.0576477E-02 at 170iterations 6.5476599E-04 1.2394428E-02 at 180iterations finished qdiffx linear iterations at : 14:55:31 total time elapsed so far: 15.82000 # loops : 180 mean,max change (kT/e) : 6.5476599E-04 1.2394428E-02 energy calculations done at 15.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.00000 DelPhi exited at 14:55:31 16.002u 0.301s 0:16.62 98.0% 0+0k 0+0io 0pf+0w