Sun Oct 9 23:41:52 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 23:41:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2815 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5417414 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): -40.67200 25.04200 ymin,ymax (A): -27.75100 23.85600 zmin,zma (A): -7.627000 36.51200 x,y,z range (A): 65.71400 51.60700 44.13900 scale (grids/A): 0.5417414 object centre (A): -7.815001 -1.947500 14.44250 number of atom coordinates read : 2815 total number of charged atoms : 2673 net assigned charge : 5.000008 assigned positive charge : 429.6916 centred at (gu) : 89.86876 90.04021 89.61940 assigned negative charge : -424.6926 centred at (gu) : 89.92562 90.13162 89.56153 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5361 nv = 96 ne = 84 npr = 54540 no. pairs analyzed = 54540 no. exposed pairs = 3775 no. arc points = 27963 no. surface atoms = 1251 nbur = 1564 mkacc time = 8.9999996E-02 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= 196 mr = 2545 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3006 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2851 ## 475 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7104 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7061519E-11 5.2433374E-10 midg,1,midg; midg,igrid,midg 7.4686246E-10 -2.3825941E-10 1,midg,midg; igrid,midg,midg 5.8970684E-10 -4.3211153E-11 gauss-seidel spectral radius is 0.9824306 estimated iterations to convergence 62 setup time was (sec) 0.3900000 now iterating at: 23:41:52 rms-change max change #iterations 7.0010088E-02 13.09458 at 10iterations 4.4573615E-03 0.7927399 at 20iterations 2.8646132E-04 5.1185608E-02 at 30iterations 1.8551171E-05 3.4408569E-03 at 40iterations 1.2697253E-06 2.3651123E-04 at 50iterations finished qdiffx linear iterations at : 23:41:55 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.2697253E-06 2.3651123E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 23:41:56 3.466u 0.167s 0:03.94 91.8% 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 Sun Oct 9 2011 at 23:41:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2815 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.625224 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): -40.67200 25.04200 ymin,ymax (A): -27.75100 23.85600 zmin,zma (A): -7.627000 36.51200 x,y,z range (A): 65.71400 51.60700 44.13900 scale (grids/A): 1.625224 object centre (A): -7.815001 -1.947500 14.44250 number of atom coordinates read : 2815 total number of charged atoms : 2673 net assigned charge : 5.000008 assigned positive charge : 429.6916 centred at (gu) : 89.60595 90.12012 88.85744 assigned negative charge : -424.6926 centred at (gu) : 89.77674 90.39487 88.68443 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 59549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27963 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 16918 mr = 38275 m= 1604 mr = 11007 m= 20 mr = 653 m= 0 mr = 2 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 677 time to turn everything in is 0.2900000 number of dielectric boundary points 28154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 363 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 20413 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) : 0.5417414 object centre at (A) : -7.815001 -1.947500 14.44250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3336501E-03 6.9332711E-04 midg,1,midg; midg,igrid,midg 9.8207761E-03 2.0956066E-03 1,midg,midg; igrid,midg,midg 1.4827335E-02 1.4775186E-03 gauss-seidel spectral radius is 0.9981543 estimated iterations to convergence 185 setup time was (sec) 0.5100000 now iterating at: 23:41:57 rms-change max change #iterations 3.173402 148.4885 at 10iterations 1.301445 53.20280 at 20iterations 0.5347975 21.94699 at 30iterations 0.2210823 8.850292 at 40iterations 9.0952352E-02 3.706256 at 50iterations 3.7682038E-02 1.400890 at 60iterations 1.5553738E-02 0.6338272 at 70iterations 6.4229029E-03 0.2533283 at 80iterations 2.6443044E-03 0.1006031 at 90iterations 1.0924123E-03 4.3601990E-02 at 100iterations 4.5201194E-04 1.7601132E-02 at 110iterations 1.8676725E-04 6.8301260E-03 at 120iterations finished qdiffx linear iterations at : 23:42:04 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 1.8676725E-04 6.8301260E-03 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 23:42:04 7.741u 0.189s 0:08.26 95.8% 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 Sun Oct 9 2011 at 23:42:04 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2815 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.437836 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): -40.67200 25.04200 ymin,ymax (A): -27.75100 23.85600 zmin,zma (A): -7.627000 36.51200 x,y,z range (A): 65.71400 51.60700 44.13900 scale (grids/A): 2.437836 object centre (A): -7.815001 -1.947500 14.44250 number of atom coordinates read : 2815 total number of charged atoms : 2673 net assigned charge : 5.000008 assigned positive charge : 429.6916 centred at (gu) : 89.40880 90.18008 88.28585 assigned negative charge : -424.6926 centred at (gu) : 89.66514 90.59222 88.02647 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 138676 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27963 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 59161 mr = 94215 m= 15657 mr = 45481 m= 2306 mr = 11219 m= 97 mr = 1439 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 2237 time to turn everything in is 0.7100000 number of dielectric boundary points 63525 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 21356 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) : 1.625224 object centre at (A) : -7.815001 -1.947500 14.44250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4921578E-03 9.4834631E-03 midg,1,midg; midg,igrid,midg 0.1573027 8.0611020E-02 1,midg,midg; igrid,midg,midg 9.5975511E-02 -3.0139500E-02 gauss-seidel spectral radius is 0.9991245 estimated iterations to convergence 267 setup time was (sec) 0.9400000 now iterating at: 23:42:05 rms-change max change #iterations 8.161569 369.1719 at 10iterations 4.453333 127.1983 at 20iterations 2.448131 69.11580 at 30iterations 1.336980 29.36696 at 40iterations 0.7315140 16.49249 at 50iterations 0.3996553 9.211168 at 60iterations 0.2172115 4.786442 at 70iterations 0.1185707 2.897216 at 80iterations 6.4731047E-02 1.318055 at 90iterations 3.5308726E-02 0.8029113 at 100iterations 1.9209869E-02 0.4102516 at 110iterations 1.0489983E-02 0.2662659 at 120iterations 5.7148980E-03 0.1203394 at 130iterations 3.1213369E-03 7.1952820E-02 at 140iterations 1.7008416E-03 3.5986900E-02 at 150iterations 9.2689210E-04 2.2817612E-02 at 160iterations 5.0446263E-04 1.1358261E-02 at 170iterations 2.7613877E-04 6.1285496E-03 at 180iterations finished qdiffx linear iterations at : 23:42:16 total time elapsed so far: 11.99000 # loops : 180 mean,max change (kT/e) : 2.7613877E-04 6.1285496E-03 energy calculations done at 11.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 23:42:17 12.124u 0.202s 0:12.67 97.2% 0+0k 0+0io 0pf+0w