Tue Oct 11 06:01:45 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 06:01:45 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 = 2030 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7296876 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): -8.906000 38.06500 ymin,ymax (A): -28.85500 19.93300 zmin,zma (A): 3.848000 46.24700 x,y,z range (A): 46.97100 48.78800 42.39900 scale (grids/A): 0.7296876 object centre (A): 14.57950 -4.460999 25.04750 number of atom coordinates read : 2030 total number of charged atoms : 1920 net assigned charge : 7.500009 assigned positive charge : 310.7490 centred at (gu) : 90.94074 88.91367 90.14050 assigned negative charge : -303.2492 centred at (gu) : 90.82101 89.02876 90.21368 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7417 nv = 96 ne = 84 npr = 40296 no. pairs analyzed = 40296 no. exposed pairs = 2469 no. arc points = 17004 no. surface atoms = 841 nbur = 1189 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 568 mr = 4316 m= 0 mr = 104 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.2800000 number of dielectric boundary points 3565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1576 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8024 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5568904E-07 4.7229477E-08 midg,1,midg; midg,igrid,midg 2.3550976E-07 1.1633593E-08 1,midg,midg; igrid,midg,midg 8.7350376E-09 2.3331665E-07 gauss-seidel spectral radius is 0.9902012 estimated iterations to convergence 82 setup time was (sec) 0.5800000 now iterating at: 06:01:46 rms-change max change #iterations 0.2269588 37.69287 at 10iterations 2.9741146E-02 4.049850 at 20iterations 4.0088762E-03 0.5015965 at 30iterations 6.0717034E-04 9.5153809E-02 at 40iterations 1.2260307E-04 1.5558243E-02 at 50iterations finished qdiffx linear iterations at : 06:01:49 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 1.2260307E-04 1.5558243E-02 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 06:01:49 4.032u 0.240s 0:04.60 92.8% 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 06:01:49 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 = 2030 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: 2.189063 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): -8.906000 38.06500 ymin,ymax (A): -28.85500 19.93300 zmin,zma (A): 3.848000 46.24700 x,y,z range (A): 46.97100 48.78800 42.39900 scale (grids/A): 2.189063 object centre (A): 14.57950 -4.460999 25.04750 number of atom coordinates read : 2030 total number of charged atoms : 1920 net assigned charge : 7.500009 assigned positive charge : 310.7490 centred at (gu) : 92.82226 86.74075 90.42152 assigned negative charge : -303.2492 centred at (gu) : 92.46311 87.08633 90.64113 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78488 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17004 grid for indexing accessible points = 1.400000 m= 32734 mr = 55773 m= 6737 mr = 25191 m= 640 mr = 4548 m= 26 mr = 312 m= 0 mr = 2 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 610 time to turn everything in is 0.6400000 number of dielectric boundary points 32799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15281 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) : 0.7296876 object centre at (A) : 14.57950 -4.460999 25.04750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6624050E-02 2.4953041E-02 midg,1,midg; midg,igrid,midg 0.1191261 4.0384054E-02 1,midg,midg; igrid,midg,midg -3.3612926E-02 4.1635904E-02 gauss-seidel spectral radius is 0.9988890 estimated iterations to convergence 237 setup time was (sec) 1.000000 now iterating at: 06:01:51 rms-change max change #iterations 4.807349 199.6528 at 10iterations 2.416241 83.05765 at 20iterations 1.223389 36.11953 at 30iterations 0.6162928 17.20275 at 40iterations 0.3111963 9.394621 at 50iterations 0.1573927 4.248573 at 60iterations 7.9742610E-02 2.376518 at 70iterations 4.0259711E-02 1.146464 at 80iterations 2.0409619E-02 0.6186600 at 90iterations 1.0367897E-02 0.2976141 at 100iterations 5.2602887E-03 0.1597252 at 110iterations 2.7076825E-03 8.1556320E-02 at 120iterations finished qdiffx linear iterations at : 06:01:59 total time elapsed so far: 9.130000 # loops : 120 mean,max change (kT/e) : 2.7076825E-03 8.1556320E-02 energy calculations done at 9.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.340000 DelPhi exited at 06:01:59 9.347u 0.320s 0:09.99 96.6% 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 06:01:59 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 = 2030 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.283594 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): -8.906000 38.06500 ymin,ymax (A): -28.85500 19.93300 zmin,zma (A): 3.848000 46.24700 x,y,z range (A): 46.97100 48.78800 42.39900 scale (grids/A): 3.283594 object centre (A): 14.57950 -4.460999 25.04750 number of atom coordinates read : 2030 total number of charged atoms : 1920 net assigned charge : 7.500009 assigned positive charge : 310.7490 centred at (gu) : 94.23335 85.11111 90.63227 assigned negative charge : -303.2492 centred at (gu) : 93.69475 85.62950 90.96168 start vw surface at 0.1500000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 180996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17004 grid for indexing accessible points = 1.400000 m= 100846 mr = 134661 m= 42712 mr = 84329 m= 12706 mr = 35401 m= 2514 mr = 9919 m= 351 mr = 1793 m= 21 mr = 210 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 2206 time to turn everything in is 2.040000 number of dielectric boundary points 73826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 15359 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) : 2.189063 object centre at (A) : 14.57950 -4.460999 25.04750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1219603 0.2122431 midg,1,midg; midg,igrid,midg 1.009448 0.2647567 1,midg,midg; igrid,midg,midg -0.3882745 0.3091260 gauss-seidel spectral radius is 0.9993130 estimated iterations to convergence 301 setup time was (sec) 2.400000 now iterating at: 06:02:02 rms-change max change #iterations 10.57045 336.3171 at 10iterations 6.300205 129.8433 at 20iterations 3.758821 75.19212 at 30iterations 2.235727 48.59679 at 40iterations 1.328183 25.66915 at 50iterations 0.7862366 15.98510 at 60iterations 0.4644343 8.484219 at 70iterations 0.2745607 5.088275 at 80iterations 0.1618506 3.033817 at 90iterations 9.5438726E-02 1.597870 at 100iterations 5.6418825E-02 1.049686 at 110iterations 3.3354543E-02 0.5428381 at 120iterations 1.9803712E-02 0.3723316 at 130iterations 1.1829894E-02 0.2257500 at 140iterations 7.1819131E-03 0.1335497 at 150iterations 4.4552065E-03 8.1459045E-02 at 160iterations 2.8600583E-03 5.2650452E-02 at 170iterations 1.9434094E-03 3.5942078E-02 at 180iterations finished qdiffx linear iterations at : 06:02:15 total time elapsed so far: 14.80000 # loops : 180 mean,max change (kT/e) : 1.9434094E-03 3.5942078E-02 energy calculations done at 14.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.02000 DelPhi exited at 06:02:16 15.025u 0.293s 0:16.30 93.9% 0+0k 0+0io 0pf+0w