Sat Oct 8 17:12:26 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 17:12:26 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3403 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: 0.5530354 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): 37.66000 94.87500 ymin,ymax (A): 16.67700 81.04900 zmin,zma (A): -23.16200 25.57300 x,y,z range (A): 57.21500 64.37200 48.73500 scale (grids/A): 0.5530354 object centre (A): 66.26750 48.86300 1.205501 number of atom coordinates read : 3403 total number of charged atoms : 3257 net assigned charge : -6.499984 assigned positive charge : 510.7315 centred at (gu) : 90.04786 89.99148 89.87103 assigned negative charge : -517.2327 centred at (gu) : 90.05547 89.97208 89.84106 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6793 nv = 96 ne = 84 npr = 68453 no. pairs analyzed = 68453 no. exposed pairs = 4292 no. arc points = 29487 no. surface atoms = 1434 nbur = 1969 mkacc time = 0.1500000 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= 297 mr = 3657 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3400000 number of dielectric boundary points 3411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2989 ## 414 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8852 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6007557E-10 -2.2518537E-10 midg,1,midg; midg,igrid,midg -7.2839124E-10 -3.3655218E-10 1,midg,midg; igrid,midg,midg -4.5016038E-10 -6.1503957E-10 gauss-seidel spectral radius is 0.9831699 estimated iterations to convergence 63 setup time was (sec) 0.5700000 now iterating at: 17:12:27 rms-change max change #iterations 8.6689658E-02 15.02930 at 10iterations 6.0143457E-03 0.9051523 at 20iterations 4.7667857E-04 7.3150158E-02 at 30iterations 5.5726436E-05 8.9902878E-03 at 40iterations 1.1611577E-05 2.1705627E-03 at 50iterations finished qdiffx linear iterations at : 17:12:29 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 1.1611577E-05 2.1705627E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 17:12:30 3.301u 0.206s 0:03.80 92.1% 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 17:12:30 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3403 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: 1.659106 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): 37.66000 94.87500 ymin,ymax (A): 16.67700 81.04900 zmin,zma (A): -23.16200 25.57300 x,y,z range (A): 57.21500 64.37200 48.73500 scale (grids/A): 1.659106 object centre (A): 66.26750 48.86300 1.205501 number of atom coordinates read : 3403 total number of charged atoms : 3257 net assigned charge : -6.499984 assigned positive charge : 510.7315 centred at (gu) : 90.14296 89.97333 89.61211 assigned negative charge : -517.2327 centred at (gu) : 90.16574 89.91563 89.52277 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29487 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 24551 mr = 52152 m= 2715 mr = 17256 m= 74 mr = 1370 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 403 time to turn everything in is 0.5300000 number of dielectric boundary points 31951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 376 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 25047 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) : 0.5530354 object centre at (A) : 66.26750 48.86300 1.205501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.3387828E-03 -4.2445753E-03 midg,1,midg; midg,igrid,midg 9.1974512E-03 1.6543584E-02 1,midg,midg; igrid,midg,midg -1.7531332E-02 -7.0226793E-03 gauss-seidel spectral radius is 0.9982866 estimated iterations to convergence 192 setup time was (sec) 0.8200000 now iterating at: 17:12:31 rms-change max change #iterations 3.738002 174.2700 at 10iterations 1.599004 58.33703 at 20iterations 0.6832952 23.03526 at 30iterations 0.2927666 10.66820 at 40iterations 0.1252193 4.169608 at 50iterations 5.3612962E-02 1.861714 at 60iterations 2.2988955E-02 0.7464650 at 70iterations 9.8580951E-03 0.3237190 at 80iterations 4.2365398E-03 0.1306095 at 90iterations 1.8157164E-03 6.3841738E-02 at 100iterations 7.8352581E-04 2.6540071E-02 at 110iterations 3.4210482E-04 1.1926651E-02 at 120iterations finished qdiffx linear iterations at : 17:12:37 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 3.4210482E-04 1.1926651E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 17:12:38 7.496u 0.232s 0:08.01 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 17:12:38 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3403 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: 2.488660 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): 37.66000 94.87500 ymin,ymax (A): 16.67700 81.04900 zmin,zma (A): -23.16200 25.57300 x,y,z range (A): 57.21500 64.37200 48.73500 scale (grids/A): 2.488660 object centre (A): 66.26750 48.86300 1.205501 number of atom coordinates read : 3403 total number of charged atoms : 3257 net assigned charge : -6.499984 assigned positive charge : 510.7315 centred at (gu) : 90.21422 89.95975 89.41807 assigned negative charge : -517.2327 centred at (gu) : 90.24854 89.87336 89.28413 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 174740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29487 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 84127 mr = 127008 m= 25334 mr = 67388 m= 4317 mr = 19357 m= 369 mr = 2907 m= 8 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 1349 time to turn everything in is 1.310000 number of dielectric boundary points 72055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 26029 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) : 1.659106 object centre at (A) : 66.26750 48.86300 1.205501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7373041E-02 -3.3741351E-02 midg,1,midg; midg,igrid,midg 0.2470470 0.5426596 1,midg,midg; igrid,midg,midg -0.2565715 -6.6540182E-02 gauss-seidel spectral radius is 0.9991761 estimated iterations to convergence 275 setup time was (sec) 1.620000 now iterating at: 17:12:40 rms-change max change #iterations 9.473434 460.1910 at 10iterations 5.372371 112.7944 at 20iterations 3.027647 64.53930 at 30iterations 1.701036 33.49252 at 40iterations 0.9535191 19.32476 at 50iterations 0.5339406 10.02579 at 60iterations 0.2977650 5.797904 at 70iterations 0.1666794 3.093658 at 80iterations 9.3065873E-02 1.774906 at 90iterations 5.2016083E-02 0.9949913 at 100iterations 2.8898554E-02 0.5878754 at 110iterations 1.6128950E-02 0.2893124 at 120iterations 8.9957127E-03 0.1654432 at 130iterations 5.0066491E-03 9.3030795E-02 at 140iterations 2.7957258E-03 4.8766136E-02 at 150iterations 1.5613185E-03 2.8726578E-02 at 160iterations 8.7395241E-04 1.7183304E-02 at 170iterations 4.8862264E-04 9.4051361E-03 at 180iterations finished qdiffx linear iterations at : 17:12:50 total time elapsed so far: 12.12000 # loops : 180 mean,max change (kT/e) : 4.8862264E-04 9.4051361E-03 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 17:12:51 12.293u 0.236s 0:12.80 97.8% 0+0k 0+0io 0pf+0w