Fri Feb 3 15:37:50 PST 2012 #!/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 Fri Feb 3 2012 at 15:37:50 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 ! Automatically converted by prot2crg.py # of charge parameter records: 939 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4409 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: 0.5340614 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): 3.010000 61.91800 ymin,ymax (A): -50.06500 16.59400 zmin,zma (A): -7.308000 53.74900 x,y,z range (A): 58.90800 66.65900 61.05700 scale (grids/A): 0.5340614 object centre (A): 32.46400 -16.73550 23.22050 number of atom coordinates read : 4409 total number of charged atoms : 4261 net assigned charge : 1.000026 assigned positive charge : 651.7285 centred at (gu) : 90.02456 88.53981 91.75305 assigned negative charge : -650.7325 centred at (gu) : 89.94637 88.42168 91.76270 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8199 nv = 96 ne = 84 npr = 88796 no. pairs analyzed = 88796 no. exposed pairs = 5680 no. arc points = 40344 no. surface atoms = 1909 nbur = 2500 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 = 1.596000 m= 307 mr = 4142 m= 3 mr = 10 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 0.3600000 number of dielectric boundary points 4357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4085 ## 524 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 10867 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.1523586E-11 -1.2777833E-11 midg,1,midg; midg,igrid,midg -9.9814990E-10 5.2768562E-10 1,midg,midg; igrid,midg,midg -4.2913906E-10 5.2928989E-10 gauss-seidel spectral radius is 0.9820519 estimated iterations to convergence 62 setup time was (sec) 0.5700000 now iterating at: 15:37:51 rms-change max change #iterations 7.8592397E-02 12.37687 at 10iterations 5.1297601E-03 0.7979736 at 20iterations 4.0298520E-04 6.9587708E-02 at 30iterations 6.2901709E-05 8.0432892E-03 at 40iterations 1.4791171E-05 1.8672943E-03 at 50iterations finished qdiffx linear iterations at : 15:37:54 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 1.4791171E-05 1.8672943E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 15:37:55 3.695u 0.171s 0:04.30 89.7% 0+0k 0+46512io 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 Fri Feb 3 2012 at 15:37:55 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 ! Automatically converted by prot2crg.py # of charge parameter records: 939 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4409 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: 1.602184 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): 3.010000 61.91800 ymin,ymax (A): -50.06500 16.59400 zmin,zma (A): -7.308000 53.74900 x,y,z range (A): 58.90800 66.65900 61.05700 scale (grids/A): 1.602184 object centre (A): 32.46400 -16.73550 23.22050 number of atom coordinates read : 4409 total number of charged atoms : 4261 net assigned charge : 1.000026 assigned positive charge : 651.7285 centred at (gu) : 90.07209 85.61815 95.25764 assigned negative charge : -650.7325 centred at (gu) : 89.83867 85.26452 95.28777 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 91603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40344 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 28223 mr = 61486 m= 3141 mr = 19284 m= 75 mr = 1504 m= 0 mr = 2 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 359 time to turn everything in is 0.5500000 number of dielectric boundary points 40766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 414 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 32523 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) : 0.5340614 object centre at (A) : 32.46400 -16.73550 23.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0134617E-03 1.3520853E-02 midg,1,midg; midg,igrid,midg -3.8373176E-02 1.2359025E-02 1,midg,midg; igrid,midg,midg -1.8211117E-02 1.7085267E-02 gauss-seidel spectral radius is 0.9982803 estimated iterations to convergence 191 setup time was (sec) 0.7600000 now iterating at: 15:37:56 rms-change max change #iterations 4.002197 150.6027 at 10iterations 1.695891 57.49159 at 20iterations 0.7245356 23.90491 at 30iterations 0.3088543 9.069028 at 40iterations 0.1322678 3.765204 at 50iterations 5.6383241E-02 1.685599 at 60iterations 2.4014397E-02 0.7291260 at 70iterations 1.0256233E-02 0.3163414 at 80iterations 4.3938574E-03 0.1458817 at 90iterations 1.8778570E-03 5.4969788E-02 at 100iterations 8.0467603E-04 2.5989532E-02 at 110iterations 3.4529692E-04 1.1282921E-02 at 120iterations finished qdiffx linear iterations at : 15:38:03 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 3.4529692E-04 1.1282921E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 15:38:04 8.243u 0.218s 0:08.98 94.0% 0+0k 0+45536io 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 Fri Feb 3 2012 at 15:38:04 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 ! Automatically converted by prot2crg.py # of charge parameter records: 939 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4409 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: 2.403276 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): 3.010000 61.91800 ymin,ymax (A): -50.06500 16.59400 zmin,zma (A): -7.308000 53.74900 x,y,z range (A): 58.90800 66.65900 61.05700 scale (grids/A): 2.403276 object centre (A): 32.46400 -16.73550 23.22050 number of atom coordinates read : 4409 total number of charged atoms : 4261 net assigned charge : 1.000026 assigned positive charge : 651.7285 centred at (gu) : 90.10806 83.42678 97.88617 assigned negative charge : -650.7325 centred at (gu) : 89.75785 82.89675 97.93159 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 213223 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40344 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 96990 mr = 151555 m= 28587 mr = 75904 m= 4847 mr = 21230 m= 330 mr = 3159 m= 1 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1126 time to turn everything in is 1.400000 number of dielectric boundary points 92010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 34044 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) : 1.602184 object centre at (A) : 32.46400 -16.73550 23.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1797159 0.3205493 midg,1,midg; midg,igrid,midg -0.9539186 0.2132440 1,midg,midg; igrid,midg,midg -0.3342412 0.3191607 gauss-seidel spectral radius is 0.9992123 estimated iterations to convergence 281 setup time was (sec) 1.640000 now iterating at: 15:38:06 rms-change max change #iterations 10.57206 336.6517 at 10iterations 6.153213 139.0659 at 20iterations 3.563352 71.66331 at 30iterations 2.045255 41.06761 at 40iterations 1.171874 22.59241 at 50iterations 0.6689442 12.99487 at 60iterations 0.3804500 7.175928 at 70iterations 0.2163071 4.226271 at 80iterations 0.1230029 2.351860 at 90iterations 6.9574945E-02 1.434566 at 100iterations 3.9420754E-02 0.6991997 at 110iterations 2.2305449E-02 0.4187355 at 120iterations 1.2635526E-02 0.2260704 at 130iterations 7.1332031E-03 0.1348028 at 140iterations 4.0311748E-03 7.5244904E-02 at 150iterations 2.2818886E-03 4.1905880E-02 at 160iterations 1.2882814E-03 2.3696899E-02 at 170iterations 7.2850898E-04 1.3454199E-02 at 180iterations finished qdiffx linear iterations at : 15:38:17 total time elapsed so far: 13.38000 # loops : 180 mean,max change (kT/e) : 7.2850898E-04 1.3454199E-02 energy calculations done at 13.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.52000 DelPhi exited at 15:38:18 13.525u 0.221s 0:14.08 97.5% 0+0k 0+45528io 0pf+0w