Wed Feb 15 08:54:47 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:48 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 ! Automatically converted by prot2crg.py # of charge parameter records: 952 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3109 !!! WARNING: TPO 162 has a net charge of -1.7500 !!! WARNING: TPO 301 has a net charge of -1.7500 !!! WARNING: SEP 320 has a net charge of -1.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6026034 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): 7.679000 63.00700 ymin,ymax (A): 22.76800 81.84500 zmin,zma (A): 5.895000 61.21600 x,y,z range (A): 55.32800 59.07700 55.32100 scale (grids/A): 0.6026034 object centre (A): 35.34300 52.30650 33.55550 number of atom coordinates read : 3109 total number of charged atoms : 2959 net assigned charge : -16.00001 assigned positive charge : 455.1051 centred at (gu) : 89.26186 89.36907 89.07644 assigned negative charge : -471.1059 centred at (gu) : 89.38224 89.36119 88.83179 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7881 nv = 96 ne = 84 npr = 61476 no. pairs analyzed = 61476 no. exposed pairs = 4370 no. arc points = 31538 no. surface atoms = 1463 nbur = 1646 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3927 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 4337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3116 ## 277 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 9586 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3942937E-08 3.2117471E-09 midg,1,midg; midg,igrid,midg -8.8782066E-09 -6.0809664E-09 1,midg,midg; igrid,midg,midg -1.8961859E-09 -1.1196547E-08 gauss-seidel spectral radius is 0.9858096 estimated iterations to convergence 69 setup time was (sec) 0.6200000 now iterating at: 08:54:49 rms-change max change #iterations 0.1217458 19.01193 at 10iterations 1.0720552E-02 1.587947 at 20iterations 1.3226682E-03 0.2436905 at 30iterations 3.6803997E-04 7.2261810E-02 at 40iterations 1.3558952E-04 2.7137756E-02 at 50iterations finished qdiffx linear iterations at : 08:54:52 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 1.3558952E-04 2.7137756E-02 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 08:54:56 4.351u 0.437s 0:08.80 54.3% 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 Wed Feb 15 2012 at 08:54:57 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 ! Automatically converted by prot2crg.py # of charge parameter records: 952 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3109 !!! WARNING: TPO 162 has a net charge of -1.7500 !!! WARNING: TPO 301 has a net charge of -1.7500 !!! WARNING: SEP 320 has a net charge of -1.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.807810 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): 7.679000 63.00700 ymin,ymax (A): 22.76800 81.84500 zmin,zma (A): 5.895000 61.21600 x,y,z range (A): 55.32800 59.07700 55.32100 scale (grids/A): 1.807810 object centre (A): 35.34300 52.30650 33.55550 number of atom coordinates read : 3109 total number of charged atoms : 2959 net assigned charge : -16.00001 assigned positive charge : 455.1051 centred at (gu) : 87.78507 88.10635 87.22867 assigned negative charge : -471.1059 centred at (gu) : 88.14614 88.08325 86.49494 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84772 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31538 grid for indexing accessible points = 1.400000 m= 29001 mr = 55413 m= 3885 mr = 20159 m= 178 mr = 2035 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 40186 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 23186 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) : 0.6026034 object centre at (A) : 35.34300 52.30650 33.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5978684E-02 2.5107481E-03 midg,1,midg; midg,igrid,midg -1.4125436E-02 -1.8751148E-02 1,midg,midg; igrid,midg,midg -1.6536022E-02 -4.2785894E-02 gauss-seidel spectral radius is 0.9985654 estimated iterations to convergence 209 setup time was (sec) 0.6800000 now iterating at: 08:54:58 rms-change max change #iterations 4.279696 189.1327 at 10iterations 1.962718 75.60885 at 20iterations 0.8928667 28.70685 at 30iterations 0.4102899 14.30656 at 40iterations 0.1882301 6.502502 at 50iterations 8.6201034E-02 2.842174 at 60iterations 3.9613634E-02 1.202116 at 70iterations 1.8327598E-02 0.6282933 at 80iterations 8.4988018E-03 0.2559204 at 90iterations 4.0279920E-03 0.1392698 at 100iterations 1.9708660E-03 6.7735672E-02 at 110iterations 1.0414475E-03 4.6842575E-02 at 120iterations finished qdiffx linear iterations at : 08:55:06 total time elapsed so far: 9.450000 # loops : 120 mean,max change (kT/e) : 1.0414475E-03 4.6842575E-02 energy calculations done at 9.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.580000 DelPhi exited at 08:55:07 9.582u 0.272s 0:10.54 93.4% 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 Wed Feb 15 2012 at 08:55:07 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 ! Automatically converted by prot2crg.py # of charge parameter records: 952 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3109 !!! WARNING: TPO 162 has a net charge of -1.7500 !!! WARNING: TPO 301 has a net charge of -1.7500 !!! WARNING: SEP 320 has a net charge of -1.5000 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: 2.711715 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): 7.679000 63.00700 ymin,ymax (A): 22.76800 81.84500 zmin,zma (A): 5.895000 61.21600 x,y,z range (A): 55.32800 59.07700 55.32100 scale (grids/A): 2.711715 object centre (A): 35.34300 52.30650 33.55550 number of atom coordinates read : 3109 total number of charged atoms : 2959 net assigned charge : -16.00001 assigned positive charge : 455.1051 centred at (gu) : 86.67735 87.15923 85.84266 assigned negative charge : -471.1059 centred at (gu) : 87.21903 87.12462 84.74221 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 196053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31538 grid for indexing accessible points = 1.400000 m= 95017 mr = 135656 m= 31915 mr = 74785 m= 6534 mr = 24429 m= 714 mr = 4363 m= 29 mr = 371 m= 0 mr = 3 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 90655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 23666 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) : 1.807810 object centre at (A) : 35.34300 52.30650 33.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6648772 8.1908911E-02 midg,1,midg; midg,igrid,midg -4.8701119E-02 -0.2190699 1,midg,midg; igrid,midg,midg -0.2589611 -0.3795016 gauss-seidel spectral radius is 0.9992663 estimated iterations to convergence 291 setup time was (sec) 1.310000 now iterating at: 08:55:09 rms-change max change #iterations 10.50058 317.7892 at 10iterations 6.243932 138.3170 at 20iterations 3.661826 83.58237 at 30iterations 2.138455 41.30322 at 40iterations 1.244345 25.95735 at 50iterations 0.7230418 13.17847 at 60iterations 0.4184817 7.576640 at 70iterations 0.2416078 4.296265 at 80iterations 0.1398467 2.686799 at 90iterations 8.0911539E-02 1.394379 at 100iterations 4.6640966E-02 0.8472652 at 110iterations 2.6986824E-02 0.5122375 at 120iterations 1.5579868E-02 0.3211365 at 130iterations 9.0272250E-03 0.1871490 at 140iterations 5.2468171E-03 9.8171234E-02 at 150iterations 3.0791378E-03 6.8828583E-02 at 160iterations 1.8364138E-03 4.3054581E-02 at 170iterations 1.1314109E-03 2.3323059E-02 at 180iterations finished qdiffx linear iterations at : 08:55:21 total time elapsed so far: 13.13000 # loops : 180 mean,max change (kT/e) : 1.1314109E-03 2.3323059E-02 energy calculations done at 13.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 08:55:21 13.264u 0.279s 0:13.89 97.4% 0+0k 0+0io 0pf+0w