Sat Oct 8 13:56:09 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 13:56:09 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3018 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 350 has a net charge of -3.0000 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: 0.6336210 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): 14.75300 70.93800 ymin,ymax (A): 11.49200 56.23400 zmin,zma (A): -11.28700 44.53700 x,y,z range (A): 56.18501 44.74200 55.82400 scale (grids/A): 0.6336210 object centre (A): 42.84550 33.86300 16.62500 number of atom coordinates read : 3018 total number of charged atoms : 2871 net assigned charge : -1.985993 assigned positive charge : 453.4136 centred at (gu) : 91.68296 90.39366 88.82886 assigned negative charge : -455.4002 centred at (gu) : 91.61536 90.48726 88.78616 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8008 nv = 96 ne = 84 npr = 63128 no. pairs analyzed = 63128 no. exposed pairs = 3527 no. arc points = 24184 no. surface atoms = 1194 nbur = 1824 mkacc time = 0.2000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 411 mr = 4611 m= 3 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.4400000 number of dielectric boundary points 3762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2384 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 9808 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.4507904E-09 1.8635633E-09 midg,1,midg; midg,igrid,midg 7.4861104E-09 -1.4418022E-08 1,midg,midg; igrid,midg,midg -7.1014590E-09 7.7078903E-09 gauss-seidel spectral radius is 0.9871269 estimated iterations to convergence 72 setup time was (sec) 0.7900000 now iterating at: 13:56:10 rms-change max change #iterations 0.1514065 21.16990 at 10iterations 1.4881940E-02 2.093371 at 20iterations 1.4586193E-03 0.1835480 at 30iterations 1.4687447E-04 1.8383026E-02 at 40iterations 1.6166954E-05 2.0828247E-03 at 50iterations finished qdiffx linear iterations at : 13:56:14 total time elapsed so far: 4.720000 # loops : 50 mean,max change (kT/e) : 1.6166954E-05 2.0828247E-03 energy calculations done at 4.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.940000 DelPhi exited at 13:56:14 4.942u 0.466s 0:05.68 95.0% 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 13:56:14 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3018 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 350 has a net charge of -3.0000 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: 1.900863 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): 14.75300 70.93800 ymin,ymax (A): 11.49200 56.23400 zmin,zma (A): -11.28700 44.53700 x,y,z range (A): 56.18501 44.74200 55.82400 scale (grids/A): 1.900863 object centre (A): 42.84550 33.86300 16.62500 number of atom coordinates read : 3018 total number of charged atoms : 2871 net assigned charge : -1.985993 assigned positive charge : 453.4136 centred at (gu) : 95.04859 91.18042 86.48610 assigned negative charge : -455.4002 centred at (gu) : 94.84594 91.46131 86.35809 start vw surface at 0.1800000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 87033 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24184 grid for indexing accessible points = 1.400000 m= 32059 mr = 62695 m= 5042 mr = 24076 m= 332 mr = 3113 m= 4 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 740 time to turn everything in is 0.8900000 number of dielectric boundary points 34474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 22640 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) : 0.6336210 object centre at (A) : 42.84550 33.86300 16.62500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4539660E-02 7.3857349E-03 midg,1,midg; midg,igrid,midg 1.1470273E-02 -2.2601869E-03 1,midg,midg; igrid,midg,midg -2.1810357E-02 8.2271183E-03 gauss-seidel spectral radius is 0.9986622 estimated iterations to convergence 217 setup time was (sec) 1.230000 now iterating at: 13:56:16 rms-change max change #iterations 4.636774 185.2139 at 10iterations 2.193748 69.62484 at 20iterations 1.037496 30.30596 at 30iterations 0.4899026 14.22785 at 40iterations 0.2315350 6.838242 at 50iterations 0.1095410 3.560101 at 60iterations 5.1707663E-02 1.529202 at 70iterations 2.4439923E-02 0.6795998 at 80iterations 1.1548744E-02 0.3303308 at 90iterations 5.4682367E-03 0.1782475 at 100iterations 2.5876481E-03 8.0028534E-02 at 110iterations 1.2261008E-03 3.5705566E-02 at 120iterations finished qdiffx linear iterations at : 13:56:26 total time elapsed so far: 11.38000 # loops : 120 mean,max change (kT/e) : 1.2261008E-03 3.5705566E-02 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 13:56:27 11.605u 0.515s 0:12.39 97.7% 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 13:56:27 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3018 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 350 has a net charge of -3.0000 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: 2.851295 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): 14.75300 70.93800 ymin,ymax (A): 11.49200 56.23400 zmin,zma (A): -11.28700 44.53700 x,y,z range (A): 56.18501 44.74200 55.82400 scale (grids/A): 2.851295 object centre (A): 42.84550 33.86300 16.62500 number of atom coordinates read : 3018 total number of charged atoms : 2871 net assigned charge : -1.985993 assigned positive charge : 453.4136 centred at (gu) : 97.57246 91.77055 84.72897 assigned negative charge : -455.4002 centred at (gu) : 97.26868 92.19197 84.53707 start vw surface at 0.1700000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 201809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24184 grid for indexing accessible points = 1.400000 m= 104343 mr = 151787 m= 37909 mr = 86663 m= 9021 mr = 30568 m= 1310 mr = 6649 m= 86 mr = 881 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 1.440000 no. cavity mid-points inaccessible to solvent = 2606 time to turn everything in is 2.360000 number of dielectric boundary points 77908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 2.530000 number of grid points assigned charge 22966 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) : 1.900863 object centre at (A) : 42.84550 33.86300 16.62500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6369525 0.1266116 midg,1,midg; midg,igrid,midg 0.1223796 1.2151407E-02 1,midg,midg; igrid,midg,midg -0.1026171 0.1423368 gauss-seidel spectral radius is 0.9992694 estimated iterations to convergence 292 setup time was (sec) 2.750000 now iterating at: 13:56:30 rms-change max change #iterations 10.80520 419.4900 at 10iterations 6.332267 139.1165 at 20iterations 3.684000 69.79077 at 30iterations 2.145714 38.42926 at 40iterations 1.244906 24.12518 at 50iterations 0.7208830 12.87549 at 60iterations 0.4167584 7.561983 at 70iterations 0.2407512 3.918480 at 80iterations 0.1393894 2.834183 at 90iterations 8.0411278E-02 1.356108 at 100iterations 4.6495497E-02 0.7563345 at 110iterations 2.6851458E-02 0.4758015 at 120iterations 1.5464409E-02 0.2431135 at 130iterations 8.9558726E-03 0.1467361 at 140iterations 5.1552551E-03 8.7190986E-02 at 150iterations 2.9757437E-03 4.8462391E-02 at 160iterations 1.7177389E-03 2.8086662E-02 at 170iterations 9.9005748E-04 1.7368317E-02 at 180iterations finished qdiffx linear iterations at : 13:56:47 total time elapsed so far: 20.18000 # loops : 180 mean,max change (kT/e) : 9.9005748E-04 1.7368317E-02 energy calculations done at 20.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.40000 DelPhi exited at 13:56:48 20.406u 0.534s 0:21.25 98.4% 0+0k 0+0io 0pf+0w