Tue Oct 11 06:28:14 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 Tue Oct 11 2011 at 06:28:14 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 = 2048 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6853666 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): -26.85700 13.73200 ymin,ymax (A): 21.67600 65.36500 zmin,zma (A): -17.74000 34.20300 x,y,z range (A): 40.58900 43.68900 51.94300 scale (grids/A): 0.6853666 object centre (A): -6.562500 43.52050 8.231502 number of atom coordinates read : 2048 total number of charged atoms : 1920 net assigned charge : 7.500009 assigned positive charge : 310.7490 centred at (gu) : 88.76894 89.89205 90.59169 assigned negative charge : -303.2492 centred at (gu) : 88.70498 90.05742 90.60654 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6376 nv = 96 ne = 84 npr = 41388 no. pairs analyzed = 41388 no. exposed pairs = 2481 no. arc points = 16893 no. surface atoms = 845 nbur = 1203 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 3593 m= 4 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1677 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7367 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6942378E-08 3.6841335E-08 midg,1,midg; midg,igrid,midg 8.5923375E-08 -1.1088283E-08 1,midg,midg; igrid,midg,midg 2.3269298E-08 4.3600444E-08 gauss-seidel spectral radius is 0.9889050 estimated iterations to convergence 77 setup time was (sec) 0.3400000 now iterating at: 06:28:15 rms-change max change #iterations 0.1726997 24.00349 at 10iterations 1.9984180E-02 2.828815 at 20iterations 2.4224317E-03 0.3757477 at 30iterations 3.3287876E-04 5.1856995E-02 at 40iterations 5.9876042E-05 7.5159073E-03 at 50iterations finished qdiffx linear iterations at : 06:28:18 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 5.9876042E-05 7.5159073E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 06:28:18 3.322u 0.184s 0:03.88 90.2% 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 Tue Oct 11 2011 at 06:28:18 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 = 2048 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.056100 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): -26.85700 13.73200 ymin,ymax (A): 21.67600 65.36500 zmin,zma (A): -17.74000 34.20300 x,y,z range (A): 40.58900 43.68900 51.94300 scale (grids/A): 2.056100 object centre (A): -6.562500 43.52050 8.231502 number of atom coordinates read : 2048 total number of charged atoms : 1920 net assigned charge : 7.500009 assigned positive charge : 310.7490 centred at (gu) : 86.30679 89.67596 91.77514 assigned negative charge : -303.2492 centred at (gu) : 86.11504 90.17257 91.81975 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16893 grid for indexing accessible points = 1.400000 m= 26658 mr = 48446 m= 4837 mr = 19977 m= 411 mr = 3130 m= 9 mr = 186 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 28674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 15200 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) : 0.6853666 object centre at (A) : -6.562500 43.52050 8.231502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9337454E-02 5.5954918E-02 midg,1,midg; midg,igrid,midg 4.2380232E-02 5.5121300E-03 1,midg,midg; igrid,midg,midg 1.8666901E-02 1.0249737E-02 gauss-seidel spectral radius is 0.9987591 estimated iterations to convergence 225 setup time was (sec) 0.5500000 now iterating at: 06:28:19 rms-change max change #iterations 4.270231 171.9473 at 10iterations 2.082555 67.88026 at 20iterations 1.011940 35.97637 at 30iterations 0.4946984 16.66560 at 40iterations 0.2396968 7.725576 at 50iterations 0.1165059 3.699534 at 60iterations 5.6940924E-02 1.865902 at 70iterations 2.7651437E-02 0.8853035 at 80iterations 1.3535400E-02 0.4483652 at 90iterations 6.5909517E-03 0.2142811 at 100iterations 3.2404482E-03 0.1092262 at 110iterations 1.6067391E-03 5.8813095E-02 at 120iterations finished qdiffx linear iterations at : 06:28:26 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.6067391E-03 5.8813095E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 06:28:27 7.681u 0.199s 0:08.47 92.9% 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 Tue Oct 11 2011 at 06:28:27 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 = 2048 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.084150 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): -26.85700 13.73200 ymin,ymax (A): 21.67600 65.36500 zmin,zma (A): -17.74000 34.20300 x,y,z range (A): 40.58900 43.68900 51.94300 scale (grids/A): 3.084150 object centre (A): -6.562500 43.52050 8.231502 number of atom coordinates read : 2048 total number of charged atoms : 1920 net assigned charge : 7.500009 assigned positive charge : 310.7490 centred at (gu) : 84.46011 89.51403 92.66265 assigned negative charge : -303.2492 centred at (gu) : 84.17255 90.25880 92.72964 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 157949 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16893 grid for indexing accessible points = 1.400000 m= 84476 mr = 116661 m= 32793 mr = 69919 m= 9003 mr = 26591 m= 1692 mr = 6917 m= 164 mr = 1151 m= 5 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 64738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 15360 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) : 2.056100 object centre at (A) : -6.562500 43.52050 8.231502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3723191 0.5318334 midg,1,midg; midg,igrid,midg 0.3367801 5.1250387E-02 1,midg,midg; igrid,midg,midg 0.2357392 6.1378699E-02 gauss-seidel spectral radius is 0.9992765 estimated iterations to convergence 293 setup time was (sec) 1.290000 now iterating at: 06:28:28 rms-change max change #iterations 9.661217 497.3901 at 10iterations 5.667086 130.1167 at 20iterations 3.327669 66.19067 at 30iterations 1.952637 46.08426 at 40iterations 1.138616 22.90193 at 50iterations 0.6638256 12.12943 at 60iterations 0.3861290 8.542535 at 70iterations 0.2253131 4.285557 at 80iterations 0.1308354 2.554357 at 90iterations 7.6176509E-02 1.433189 at 100iterations 4.4261593E-02 0.8615799 at 110iterations 2.5823493E-02 0.4657555 at 120iterations 1.5093820E-02 0.2879143 at 130iterations 8.8823419E-03 0.1667366 at 140iterations 5.2789515E-03 9.7007751E-02 at 150iterations 3.2085539E-03 6.0594559E-02 at 160iterations 2.0198778E-03 3.6683857E-02 at 170iterations 1.3328650E-03 2.5909424E-02 at 180iterations finished qdiffx linear iterations at : 06:28:39 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 1.3328650E-03 2.5909424E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 06:28:40 12.537u 0.194s 0:13.09 97.1% 0+0k 0+0io 0pf+0w