Sat Oct 8 19:10:02 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 19:10:02 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6181628 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): -31.84900 17.96800 ymin,ymax (A): -24.76800 21.81100 zmin,zma (A): -12.44700 45.14300 x,y,z range (A): 49.81700 46.57900 57.59000 scale (grids/A): 0.6181628 object centre (A): -6.940499 -1.478500 16.34800 number of atom coordinates read : 2595 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 88.45364 89.16662 89.77828 assigned negative charge : -390.0956 centred at (gu) : 88.35083 89.20319 89.66926 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6737 nv = 96 ne = 84 npr = 52901 no. pairs analyzed = 52901 no. exposed pairs = 3114 no. arc points = 22354 no. surface atoms = 1053 nbur = 1542 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 358 mr = 3778 m= 1 mr = 49 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 0.3000000 number of dielectric boundary points 3269 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2192 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8078 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6216836E-09 9.8331165E-09 midg,1,midg; midg,igrid,midg 6.9973898E-09 1.0338541E-09 1,midg,midg; igrid,midg,midg -4.4044839E-09 7.0878792E-09 gauss-seidel spectral radius is 0.9864494 estimated iterations to convergence 70 setup time was (sec) 0.5100000 now iterating at: 19:10:03 rms-change max change #iterations 0.1295315 20.53131 at 10iterations 1.1629990E-02 2.100926 at 20iterations 1.0531998E-03 0.1402283 at 30iterations 9.8355522E-05 1.3767481E-02 at 40iterations 9.0211879E-06 1.1858940E-03 at 50iterations finished qdiffx linear iterations at : 19:10:05 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 9.0211879E-06 1.1858940E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 19:10:06 3.086u 0.155s 0:03.52 91.7% 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 19:10:06 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.854488 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): -31.84900 17.96800 ymin,ymax (A): -24.76800 21.81100 zmin,zma (A): -12.44700 45.14300 x,y,z range (A): 49.81700 46.57900 57.59000 scale (grids/A): 1.854488 object centre (A): -6.940499 -1.478500 16.34800 number of atom coordinates read : 2595 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 85.36048 87.49924 89.33432 assigned negative charge : -390.0956 centred at (gu) : 85.05248 87.60948 89.00743 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22354 grid for indexing accessible points = 1.400000 m= 26793 mr = 50143 m= 4219 mr = 20125 m= 220 mr = 2672 m= 6 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 677 time to turn everything in is 0.5100000 number of dielectric boundary points 30112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19311 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) : 0.6181628 object centre at (A) : -6.940499 -1.478500 16.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2571923E-02 2.5888819E-02 midg,1,midg; midg,igrid,midg 1.0693830E-02 3.6415288E-03 1,midg,midg; igrid,midg,midg -3.1612038E-03 3.2402597E-02 gauss-seidel spectral radius is 0.9985651 estimated iterations to convergence 209 setup time was (sec) 0.7700000 now iterating at: 19:10:07 rms-change max change #iterations 4.032770 193.5448 at 10iterations 1.853569 67.79392 at 20iterations 0.8509965 29.18271 at 30iterations 0.3904166 14.28428 at 40iterations 0.1794956 6.309362 at 50iterations 8.2536943E-02 2.817142 at 60iterations 3.7933238E-02 1.231232 at 70iterations 1.7436463E-02 0.5813446 at 80iterations 8.0277259E-03 0.2619815 at 90iterations 3.6744196E-03 0.1172638 at 100iterations 1.6926457E-03 5.6144714E-02 at 110iterations 7.7944499E-04 2.6805878E-02 at 120iterations finished qdiffx linear iterations at : 19:10:13 total time elapsed so far: 6.670000 # loops : 120 mean,max change (kT/e) : 7.7944499E-04 2.6805878E-02 energy calculations done at 6.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.830000 DelPhi exited at 19:10:13 6.836u 0.169s 0:07.29 95.8% 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 Sat Oct 8 2011 at 19:10:13 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.781733 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): -31.84900 17.96800 ymin,ymax (A): -24.76800 21.81100 zmin,zma (A): -12.44700 45.14300 x,y,z range (A): 49.81700 46.57900 57.59000 scale (grids/A): 2.781733 object centre (A): -6.940499 -1.478500 16.34800 number of atom coordinates read : 2595 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 83.04060 86.24888 89.00137 assigned negative charge : -390.0956 centred at (gu) : 82.57872 86.41414 88.51128 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 166203 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22354 grid for indexing accessible points = 1.400000 m= 86160 mr = 120989 m= 31689 mr = 71495 m= 7628 mr = 25821 m= 1025 mr = 5769 m= 40 mr = 675 m= 0 mr = 18 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 2044 time to turn everything in is 1.270000 number of dielectric boundary points 67978 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 19728 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) : 1.854488 object centre at (A) : -6.940499 -1.478500 16.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8441234E-02 0.3066964 midg,1,midg; midg,igrid,midg 0.1414785 4.1521285E-02 1,midg,midg; igrid,midg,midg -5.3918906E-03 0.4192347 gauss-seidel spectral radius is 0.9992365 estimated iterations to convergence 286 setup time was (sec) 1.530000 now iterating at: 19:10:15 rms-change max change #iterations 9.539450 302.5249 at 10iterations 5.496258 118.3865 at 20iterations 3.154473 59.45172 at 30iterations 1.800301 33.66925 at 40iterations 1.030113 21.74131 at 50iterations 0.5878786 10.60875 at 60iterations 0.3353807 6.063259 at 70iterations 0.1910834 3.569612 at 80iterations 0.1088882 2.286907 at 90iterations 6.1990157E-02 1.261292 at 100iterations 3.5193395E-02 0.6296997 at 110iterations 2.0026730E-02 0.4126740 at 120iterations 1.1435979E-02 0.2309710 at 130iterations 6.5099555E-03 0.1258855 at 140iterations 3.6987006E-03 6.7734718E-02 at 150iterations 2.1070896E-03 3.6023140E-02 at 160iterations 1.1998190E-03 2.4055481E-02 at 170iterations 6.8142626E-04 1.1856079E-02 at 180iterations finished qdiffx linear iterations at : 19:10:24 total time elapsed so far: 10.88000 # loops : 180 mean,max change (kT/e) : 6.8142626E-04 1.1856079E-02 energy calculations done at 10.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.05000 DelPhi exited at 19:10:25 11.048u 0.184s 0:11.51 97.4% 0+0k 0+0io 0pf+0w