Mon Oct 10 14:37:23 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 Mon Oct 10 2011 at 14:37:23 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 = 4391 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5696912 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): 7.781000 62.62400 ymin,ymax (A): -26.18500 34.68100 zmin,zma (A): -29.18400 33.30600 x,y,z range (A): 54.84300 60.86600 62.49000 scale (grids/A): 0.5696912 object centre (A): 35.20250 4.248000 2.061000 number of atom coordinates read : 4391 total number of charged atoms : 4244 net assigned charge : 6.000034 assigned positive charge : 654.4500 centred at (gu) : 89.91995 89.84878 89.49094 assigned negative charge : -648.4531 centred at (gu) : 89.94502 89.85850 89.58796 start vw surface at 0.2100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9234 nv = 96 ne = 84 npr = 90505 no. pairs analyzed = 90505 no. exposed pairs = 5369 no. arc points = 36041 no. surface atoms = 1811 nbur = 2580 mkacc time = 0.3000000 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 = 1.484000 m= 398 mr = 5111 m= 0 mr = 24 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.6100000 number of dielectric boundary points 4497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3660 ## 386 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 12010 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4728675E-09 -1.1712752E-09 midg,1,midg; midg,igrid,midg 1.1582938E-09 6.5425632E-10 1,midg,midg; igrid,midg,midg 1.4930287E-09 3.2173375E-10 gauss-seidel spectral radius is 0.9842045 estimated iterations to convergence 65 setup time was (sec) 0.9400000 now iterating at: 14:37:24 rms-change max change #iterations 0.1105954 13.52477 at 10iterations 8.4808450E-03 1.223272 at 20iterations 9.0118148E-04 0.1039352 at 30iterations 2.9759947E-04 3.6034584E-02 at 40iterations 1.3773353E-04 1.6655922E-02 at 50iterations finished qdiffx linear iterations at : 14:37:29 total time elapsed so far: 5.310000 # loops : 50 mean,max change (kT/e) : 1.3773353E-04 1.6655922E-02 energy calculations done at 5.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.540000 DelPhi exited at 14:37:29 5.545u 0.486s 0:06.32 95.2% 0+0k 0+0io 6pf+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 Mon Oct 10 2011 at 14:37:29 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 = 4391 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.709074 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): 7.781000 62.62400 ymin,ymax (A): -26.18500 34.68100 zmin,zma (A): -29.18400 33.30600 x,y,z range (A): 54.84300 60.86600 62.49000 scale (grids/A): 1.709074 object centre (A): 35.20250 4.248000 2.061000 number of atom coordinates read : 4391 total number of charged atoms : 4244 net assigned charge : 6.000034 assigned positive charge : 654.4500 centred at (gu) : 89.75845 89.54494 88.47127 assigned negative charge : -648.4531 centred at (gu) : 89.83430 89.57533 88.76342 start vw surface at 0.2100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 102897 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36041 grid for indexing accessible points = 1.400000 m= 35304 mr = 73832 m= 4479 mr = 25088 m= 179 mr = 2463 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 519 time to turn everything in is 1.060000 number of dielectric boundary points 41451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 309 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 32895 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) : 0.5696912 object centre at (A) : 35.20250 4.248000 2.061000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5110133E-02 -2.0375967E-02 midg,1,midg; midg,igrid,midg 3.2736532E-02 5.5972999E-03 1,midg,midg; igrid,midg,midg 7.5988569E-03 8.4253699E-03 gauss-seidel spectral radius is 0.9984866 estimated iterations to convergence 204 setup time was (sec) 1.490000 now iterating at: 14:37:31 rms-change max change #iterations 4.555285 176.3169 at 10iterations 2.051326 65.30753 at 20iterations 0.9234762 27.22362 at 30iterations 0.4158990 13.29032 at 40iterations 0.1875642 5.271332 at 50iterations 8.4815420E-02 2.489586 at 60iterations 3.8244702E-02 1.182093 at 70iterations 1.7320210E-02 0.4775982 at 80iterations 7.8786910E-03 0.2476559 at 90iterations 3.6581703E-03 9.6731186E-02 at 100iterations 1.7750567E-03 5.0728798E-02 at 110iterations 9.4135071E-04 2.9083252E-02 at 120iterations finished qdiffx linear iterations at : 14:37:43 total time elapsed so far: 12.92000 # loops : 120 mean,max change (kT/e) : 9.4135071E-04 2.9083252E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 14:37:44 13.137u 0.538s 0:14.19 96.2% 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 Mon Oct 10 2011 at 14:37:44 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 = 4391 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.563610 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): 7.781000 62.62400 ymin,ymax (A): -26.18500 34.68100 zmin,zma (A): -29.18400 33.30600 x,y,z range (A): 54.84300 60.86600 62.49000 scale (grids/A): 2.563610 object centre (A): 35.20250 4.248000 2.061000 number of atom coordinates read : 4391 total number of charged atoms : 4244 net assigned charge : 6.000034 assigned positive charge : 654.4500 centred at (gu) : 89.63747 89.31727 87.70644 assigned negative charge : -648.4531 centred at (gu) : 89.75129 89.36279 88.14489 start vw surface at 0.2100000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 239013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36041 grid for indexing accessible points = 1.400000 m= 118591 mr = 179822 m= 38176 mr = 95432 m= 7662 mr = 29668 m= 720 mr = 5380 m= 19 mr = 338 m= 0 mr = 0 time to grow re-entrant surface = 1.700000 no. cavity mid-points inaccessible to solvent = 1929 time to turn everything in is 2.700000 number of dielectric boundary points 93541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 2.870000 number of grid points assigned charge 33933 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) : 1.709074 object centre at (A) : 35.20250 4.248000 2.061000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3867864 -0.3717180 midg,1,midg; midg,igrid,midg 0.6038882 -8.8455685E-04 1,midg,midg; igrid,midg,midg 0.1564649 0.1810720 gauss-seidel spectral radius is 0.9992592 estimated iterations to convergence 290 setup time was (sec) 3.110000 now iterating at: 14:37:47 rms-change max change #iterations 11.51218 327.6133 at 10iterations 6.854760 174.4669 at 20iterations 4.056661 81.17432 at 30iterations 2.382443 44.75584 at 40iterations 1.393149 25.03154 at 50iterations 0.8105026 14.42433 at 60iterations 0.4726410 8.262077 at 70iterations 0.2748409 4.787130 at 80iterations 0.1589237 2.549671 at 90iterations 9.2186742E-02 1.457205 at 100iterations 5.3267445E-02 0.8054581 at 110iterations 3.0760689E-02 0.4732213 at 120iterations 1.7767798E-02 0.2866564 at 130iterations 1.0284031E-02 0.1787910 at 140iterations 5.9666177E-03 9.5153809E-02 at 150iterations 3.4715494E-03 5.9284210E-02 at 160iterations 2.0410097E-03 3.4189224E-02 at 170iterations 1.2267046E-03 2.0400047E-02 at 180iterations finished qdiffx linear iterations at : 14:38:07 total time elapsed so far: 22.62000 # loops : 180 mean,max change (kT/e) : 1.2267046E-03 2.0400047E-02 energy calculations done at 22.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.83000 DelPhi exited at 14:38:08 22.836u 0.600s 0:24.04 97.4% 0+0k 0+0io 0pf+0w