Sat Oct 8 18:26:34 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 18:26:34 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3573 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: 0.5548887 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): -19.97600 42.22300 ymin,ymax (A): -3.769000 56.52600 zmin,zma (A): 5.312000 69.46900 x,y,z range (A): 62.19900 60.29500 64.15701 scale (grids/A): 0.5548887 object centre (A): 11.12350 26.37850 37.39050 number of atom coordinates read : 3573 total number of charged atoms : 3429 net assigned charge : 9.000017 assigned positive charge : 539.0593 centred at (gu) : 90.02801 89.69923 90.38699 assigned negative charge : -530.0606 centred at (gu) : 90.11838 89.73527 90.37182 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7291 nv = 96 ne = 84 npr = 70217 no. pairs analyzed = 70217 no. exposed pairs = 4961 no. arc points = 35378 no. surface atoms = 1623 nbur = 1950 mkacc time = 0.1600000 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 = 1.568000 m= 364 mr = 3563 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3516 ## 423 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9459 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6821470E-10 1.0482698E-09 midg,1,midg; midg,igrid,midg 1.2728447E-09 3.6513642E-10 1,midg,midg; igrid,midg,midg 1.7605396E-09 -2.1860423E-10 gauss-seidel spectral radius is 0.9833076 estimated iterations to convergence 64 setup time was (sec) 0.6600000 now iterating at: 18:26:35 rms-change max change #iterations 8.7768376E-02 13.83957 at 10iterations 6.6423607E-03 1.031845 at 20iterations 9.0563309E-04 0.1276741 at 30iterations 2.2538251E-04 3.5037994E-02 at 40iterations 6.3154293E-05 9.8533630E-03 at 50iterations finished qdiffx linear iterations at : 18:26:39 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 6.3154293E-05 9.8533630E-03 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 18:26:39 4.496u 0.297s 0:05.09 93.9% 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 18:26:39 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3573 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.664666 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): -19.97600 42.22300 ymin,ymax (A): -3.769000 56.52600 zmin,zma (A): 5.312000 69.46900 x,y,z range (A): 62.19900 60.29500 64.15701 scale (grids/A): 1.664666 object centre (A): 11.12350 26.37850 37.39050 number of atom coordinates read : 3573 total number of charged atoms : 3429 net assigned charge : 9.000017 assigned positive charge : 539.0593 centred at (gu) : 90.08249 89.09670 91.16013 assigned negative charge : -530.0606 centred at (gu) : 90.35492 89.20540 91.11512 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 79332 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35378 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25838 mr = 51492 m= 3196 mr = 17423 m= 93 mr = 1661 m= 0 mr = 3 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 219 time to turn everything in is 0.7000000 number of dielectric boundary points 37880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 26367 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) : 0.5548887 object centre at (A) : 11.12350 26.37850 37.39050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0785305E-02 1.0454316E-02 midg,1,midg; midg,igrid,midg 3.8321319E-03 4.6238550E-03 1,midg,midg; igrid,midg,midg 1.6724505E-02 -1.4066107E-03 gauss-seidel spectral radius is 0.9983345 estimated iterations to convergence 195 setup time was (sec) 1.070000 now iterating at: 18:26:41 rms-change max change #iterations 3.875160 148.5405 at 10iterations 1.666164 59.22270 at 20iterations 0.7221838 25.04675 at 30iterations 0.3121434 10.10461 at 40iterations 0.1353921 4.461533 at 50iterations 5.8665995E-02 2.100199 at 60iterations 2.5468539E-02 0.8466415 at 70iterations 1.1140762E-02 0.3862877 at 80iterations 4.9140281E-03 0.1612396 at 90iterations 2.1826981E-03 8.9851379E-02 at 100iterations 1.0021840E-03 3.6052704E-02 at 110iterations 4.8352455E-04 1.6515732E-02 at 120iterations finished qdiffx linear iterations at : 18:26:49 total time elapsed so far: 9.800000 # loops : 120 mean,max change (kT/e) : 4.8352455E-04 1.6515732E-02 energy calculations done at 9.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.00000 DelPhi exited at 18:26:50 9.999u 0.308s 0:10.57 97.3% 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 18:26:50 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 # of charge parameter records: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3573 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: 2.496999 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): -19.97600 42.22300 ymin,ymax (A): -3.769000 56.52600 zmin,zma (A): 5.312000 69.46900 x,y,z range (A): 62.19900 60.29500 64.15701 scale (grids/A): 2.496999 object centre (A): 11.12350 26.37850 37.39050 number of atom coordinates read : 3573 total number of charged atoms : 3429 net assigned charge : 9.000017 assigned positive charge : 539.0593 centred at (gu) : 90.12343 88.64482 91.73982 assigned negative charge : -530.0606 centred at (gu) : 90.53229 88.80798 91.67262 start vw surface at 0.1700000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 183401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35378 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 86543 mr = 126398 m= 27423 mr = 66867 m= 5253 mr = 20611 m= 387 mr = 3535 m= 8 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 735 time to turn everything in is 1.610000 number of dielectric boundary points 85437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 27410 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) : 1.664666 object centre at (A) : 11.12350 26.37850 37.39050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5860059E-02 -5.1435404E-02 midg,1,midg; midg,igrid,midg -2.4970833E-02 8.7455615E-02 1,midg,midg; igrid,midg,midg 0.1719037 -3.5414733E-02 gauss-seidel spectral radius is 0.9992059 estimated iterations to convergence 280 setup time was (sec) 1.970000 now iterating at: 18:26:52 rms-change max change #iterations 9.995469 298.5245 at 10iterations 5.805464 130.1100 at 20iterations 3.347808 92.52528 at 30iterations 1.919896 40.57590 at 40iterations 1.097098 21.28279 at 50iterations 0.6245974 13.63298 at 60iterations 0.3558834 6.876046 at 70iterations 0.2014174 4.056610 at 80iterations 0.1144246 2.284623 at 90iterations 6.4702943E-02 1.270905 at 100iterations 3.6485109E-02 0.7243004 at 110iterations 2.0641051E-02 0.4003906 at 120iterations 1.1676751E-02 0.2347031 at 130iterations 6.5846541E-03 0.1224365 at 140iterations 3.7157706E-03 7.0541382E-02 at 150iterations 2.1042051E-03 3.9695740E-02 at 160iterations 1.1902592E-03 2.2796631E-02 at 170iterations 6.7460741E-04 1.2481689E-02 at 180iterations finished qdiffx linear iterations at : 18:27:06 total time elapsed so far: 15.97000 # loops : 180 mean,max change (kT/e) : 6.7460741E-04 1.2481689E-02 energy calculations done at 15.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.14000 DelPhi exited at 18:27:07 16.146u 0.275s 0:16.70 98.2% 0+0k 0+0io 0pf+0w