Tue Oct 11 06:27:58 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 06:27:58 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 = 1986 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: 0.7325706 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): -19.89800 23.87200 ymin,ymax (A): -10.14500 28.66700 zmin,zma (A): -36.75400 11.84200 x,y,z range (A): 43.77000 38.81200 48.59600 scale (grids/A): 0.7325706 object centre (A): 1.987000 9.261000 -12.45600 number of atom coordinates read : 1986 total number of charged atoms : 1908 net assigned charge : 6.500006 assigned positive charge : 307.9351 centred at (gu) : 90.00158 88.99850 91.04928 assigned negative charge : -301.4352 centred at (gu) : 89.83902 89.01717 91.14424 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7455 nv = 96 ne = 84 npr = 38506 no. pairs analyzed = 38506 no. exposed pairs = 2512 no. arc points = 17129 no. surface atoms = 846 nbur = 1140 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 553 mr = 4294 m= 7 mr = 113 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 0.2700000 number of dielectric boundary points 3608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1593 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8090 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4417738E-07 2.2514058E-08 midg,1,midg; midg,igrid,midg 1.3642729E-07 6.9221819E-08 1,midg,midg; igrid,midg,midg -3.7196234E-08 2.2931879E-07 gauss-seidel spectral radius is 0.9902746 estimated iterations to convergence 82 setup time was (sec) 0.4900000 now iterating at: 06:27:59 rms-change max change #iterations 0.2311991 39.74270 at 10iterations 3.0556137E-02 4.011780 at 20iterations 4.2120195E-03 0.5501814 at 30iterations 7.2192983E-04 8.5520029E-02 at 40iterations 1.7972336E-04 2.3303986E-02 at 50iterations finished qdiffx linear iterations at : 06:28:02 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.7972336E-04 2.3303986E-02 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 06:28:02 3.236u 0.218s 0:04.00 86.0% 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 06:28:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1986 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: 2.197712 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): -19.89800 23.87200 ymin,ymax (A): -10.14500 28.66700 zmin,zma (A): -36.75400 11.84200 x,y,z range (A): 43.77000 38.81200 48.59600 scale (grids/A): 2.197712 object centre (A): 1.987000 9.261000 -12.45600 number of atom coordinates read : 1986 total number of charged atoms : 1908 net assigned charge : 6.500006 assigned positive charge : 307.9351 centred at (gu) : 90.00462 86.99563 93.14781 assigned negative charge : -301.4352 centred at (gu) : 89.51708 87.05180 93.43285 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 78753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17129 grid for indexing accessible points = 1.400000 m= 33572 mr = 56246 m= 7135 mr = 25778 m= 749 mr = 4825 m= 22 mr = 392 m= 0 mr = 4 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 32986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15192 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) : 0.7325706 object centre at (A) : 1.987000 9.261000 -12.45600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3471619E-02 7.3584681E-03 midg,1,midg; midg,igrid,midg 4.0920585E-02 9.1480128E-03 1,midg,midg; igrid,midg,midg 2.4757933E-02 5.8341172E-02 gauss-seidel spectral radius is 0.9988937 estimated iterations to convergence 238 setup time was (sec) 0.8700000 now iterating at: 06:28:03 rms-change max change #iterations 4.824604 191.4816 at 10iterations 2.439154 88.27581 at 20iterations 1.236313 41.85956 at 30iterations 0.6285206 18.84332 at 40iterations 0.3157163 9.549765 at 50iterations 0.1607339 4.782711 at 60iterations 8.1301689E-02 2.371107 at 70iterations 4.1291736E-02 1.252140 at 80iterations 2.0970179E-02 0.6292419 at 90iterations 1.0681535E-02 0.3059921 at 100iterations 5.4645003E-03 0.1707716 at 110iterations 2.8256066E-03 8.2592010E-02 at 120iterations finished qdiffx linear iterations at : 06:28:10 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 2.8256066E-03 8.2592010E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 06:28:11 7.675u 0.257s 0:08.33 95.0% 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 06:28:11 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 = 1986 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: 3.296568 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): -19.89800 23.87200 ymin,ymax (A): -10.14500 28.66700 zmin,zma (A): -36.75400 11.84200 x,y,z range (A): 43.77000 38.81200 48.59600 scale (grids/A): 3.296568 object centre (A): 1.987000 9.261000 -12.45600 number of atom coordinates read : 1986 total number of charged atoms : 1908 net assigned charge : 6.500006 assigned positive charge : 307.9351 centred at (gu) : 90.00700 85.49346 94.72175 assigned negative charge : -301.4352 centred at (gu) : 89.27552 85.57768 95.14931 start vw surface at 0.1600000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 180830 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17129 grid for indexing accessible points = 1.400000 m= 102296 mr = 134536 m= 44191 mr = 85725 m= 13789 mr = 36664 m= 2974 mr = 10713 m= 399 mr = 2185 m= 23 mr = 283 m= 0 mr = 9 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.900000 number of dielectric boundary points 74387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 15260 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) : 2.197712 object centre at (A) : 1.987000 9.261000 -12.45600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2797690 1.6569749E-04 midg,1,midg; midg,igrid,midg 0.3088939 3.9099779E-02 1,midg,midg; igrid,midg,midg 0.4066234 0.4498357 gauss-seidel spectral radius is 0.9993119 estimated iterations to convergence 301 setup time was (sec) 2.210000 now iterating at: 06:28:13 rms-change max change #iterations 10.60272 277.3938 at 10iterations 6.325585 137.0881 at 20iterations 3.764995 88.49548 at 30iterations 2.242731 40.74568 at 40iterations 1.328338 26.81710 at 50iterations 0.7857387 15.06622 at 60iterations 0.4646649 8.671545 at 70iterations 0.2745058 4.899391 at 80iterations 0.1617642 2.806889 at 90iterations 9.5640585E-02 1.665333 at 100iterations 5.6666557E-02 0.9526978 at 110iterations 3.3545323E-02 0.5822029 at 120iterations 1.9990226E-02 0.3819351 at 130iterations 1.2076348E-02 0.2073421 at 140iterations 7.4703689E-03 0.1423779 at 150iterations 4.7932682E-03 8.3419800E-02 at 160iterations 3.2387595E-03 5.4557800E-02 at 170iterations 2.3347705E-03 3.8200378E-02 at 180iterations finished qdiffx linear iterations at : 06:28:24 total time elapsed so far: 12.93000 # loops : 180 mean,max change (kT/e) : 2.3347705E-03 3.8200378E-02 energy calculations done at 12.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 06:28:24 13.098u 0.249s 0:13.65 97.6% 0+0k 0+0io 0pf+0w