Mon Oct 10 18:38:48 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 18:38:48 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2430 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: 0.6919473 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): 29.07100 74.09600 ymin,ymax (A): 97.96100 149.0420 zmin,zma (A): 32.96900 84.41800 x,y,z range (A): 45.02500 51.08099 51.44900 scale (grids/A): 0.6919473 object centre (A): 51.58350 123.5015 58.69350 number of atom coordinates read : 2430 total number of charged atoms : 2293 net assigned charge : 2.000007 assigned positive charge : 363.7278 centred at (gu) : 89.39714 87.25992 89.08524 assigned negative charge : -361.7285 centred at (gu) : 89.27775 87.39167 89.05755 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7875 nv = 96 ne = 84 npr = 49873 no. pairs analyzed = 49873 no. exposed pairs = 3030 no. arc points = 20864 no. surface atoms = 1016 nbur = 1414 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 513 mr = 4443 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2900000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1892 ## 131 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8954 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.9136255E-10 1.7895060E-08 midg,1,midg; midg,igrid,midg 1.0916692E-07 -2.4561693E-08 1,midg,midg; igrid,midg,midg -4.2908948E-08 5.0928247E-08 gauss-seidel spectral radius is 0.9891548 estimated iterations to convergence 78 setup time was (sec) 0.5000000 now iterating at: 18:38:49 rms-change max change #iterations 0.2035640 23.26069 at 10iterations 2.4076469E-02 3.514606 at 20iterations 2.7747445E-03 0.3813362 at 30iterations 3.4507090E-04 4.4136047E-02 at 40iterations 4.5478748E-05 5.5447817E-03 at 50iterations finished qdiffx linear iterations at : 18:38:51 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 4.5478748E-05 5.5447817E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 18:38:52 3.097u 0.134s 0:03.94 81.7% 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 Mon Oct 10 2011 at 18:38:52 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 = 2430 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: 2.075842 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): 29.07100 74.09600 ymin,ymax (A): 97.96100 149.0420 zmin,zma (A): 32.96900 84.41800 x,y,z range (A): 45.02500 51.08099 51.44900 scale (grids/A): 2.075842 object centre (A): 51.58350 123.5015 58.69350 number of atom coordinates read : 2430 total number of charged atoms : 2293 net assigned charge : 2.000007 assigned positive charge : 363.7278 centred at (gu) : 88.19072 81.77909 87.25495 assigned negative charge : -361.7285 centred at (gu) : 87.83289 82.17482 87.17244 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83567 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20864 grid for indexing accessible points = 1.400000 m= 33140 mr = 58524 m= 6466 mr = 25080 m= 532 mr = 4325 m= 9 mr = 229 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 466 time to turn everything in is 0.5900000 number of dielectric boundary points 35554 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 18207 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) : 0.6919473 object centre at (A) : 51.58350 123.5015 58.69350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6025808E-02 1.3114252E-02 midg,1,midg; midg,igrid,midg 3.7490726E-02 -8.2818270E-03 1,midg,midg; igrid,midg,midg -4.5382068E-03 2.5331374E-02 gauss-seidel spectral radius is 0.9988193 estimated iterations to convergence 230 setup time was (sec) 0.8500000 now iterating at: 18:38:53 rms-change max change #iterations 4.863562 241.2989 at 10iterations 2.389454 75.04336 at 20iterations 1.183304 38.47865 at 30iterations 0.5849204 19.70476 at 40iterations 0.2884117 8.118149 at 50iterations 0.1428774 4.264852 at 60iterations 7.0393451E-02 1.961170 at 70iterations 3.4862898E-02 1.013494 at 80iterations 1.7285826E-02 0.5039766 at 90iterations 8.5106045E-03 0.2523108 at 100iterations 4.2074919E-03 0.1209810 at 110iterations 2.0801739E-03 5.6579590E-02 at 120iterations finished qdiffx linear iterations at : 18:38:59 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 2.0801739E-03 5.6579590E-02 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 18:39:00 6.963u 0.167s 0:07.61 93.5% 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 18:39:00 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 = 2430 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: 3.113763 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): 29.07100 74.09600 ymin,ymax (A): 97.96100 149.0420 zmin,zma (A): 32.96900 84.41800 x,y,z range (A): 45.02500 51.08099 51.44900 scale (grids/A): 3.113763 object centre (A): 51.58350 123.5015 58.69350 number of atom coordinates read : 2430 total number of charged atoms : 2293 net assigned charge : 2.000007 assigned positive charge : 363.7278 centred at (gu) : 87.28582 77.66863 85.88224 assigned negative charge : -361.7285 centred at (gu) : 86.74924 78.26210 85.75861 start vw surface at 0.1400000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 192763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20864 grid for indexing accessible points = 1.400000 m= 102946 mr = 141559 m= 42470 mr = 85110 m= 12245 mr = 34996 m= 2151 mr = 9482 m= 193 mr = 1444 m= 3 mr = 88 m= 0 mr = 2 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1502 time to turn everything in is 1.850000 number of dielectric boundary points 80090 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 18344 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) : 2.075842 object centre at (A) : 51.58350 123.5015 58.69350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3987366 0.4917332 midg,1,midg; midg,igrid,midg 0.2548222 -1.9215247E-02 1,midg,midg; igrid,midg,midg -4.8027311E-02 0.1393677 gauss-seidel spectral radius is 0.9993079 estimated iterations to convergence 300 setup time was (sec) 2.120000 now iterating at: 18:39:02 rms-change max change #iterations 11.01589 409.9119 at 10iterations 6.588801 146.6974 at 20iterations 3.932015 77.01786 at 30iterations 2.341799 63.92069 at 40iterations 1.389828 26.26418 at 50iterations 0.8206251 15.86703 at 60iterations 0.4846187 7.885479 at 70iterations 0.2852866 5.264771 at 80iterations 0.1678819 2.625016 at 90iterations 9.8617345E-02 1.675018 at 100iterations 5.7916652E-02 0.9501963 at 110iterations 3.3956304E-02 0.5987310 at 120iterations 1.9929472E-02 0.3106146 at 130iterations 1.1705395E-02 0.1907463 at 140iterations 6.8568056E-03 0.1170235 at 150iterations 4.0289969E-03 6.1630249E-02 at 160iterations 2.3620143E-03 3.8108826E-02 at 170iterations 1.3867755E-03 2.6138306E-02 at 180iterations finished qdiffx linear iterations at : 18:39:12 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 1.3867755E-03 2.6138306E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.10000 DelPhi exited at 18:39:12 12.106u 0.186s 0:12.77 96.1% 0+0k 0+0io 0pf+0w