Tue Oct 11 03:47:20 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 03:47:20 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2797 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6445656 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): -12.19300 37.01100 ymin,ymax (A): -26.78500 21.73600 zmin,zma (A): -9.647000 45.58400 x,y,z range (A): 49.20400 48.52100 55.23100 scale (grids/A): 0.6445656 object centre (A): 12.40900 -2.524500 17.96850 number of atom coordinates read : 2797 total number of charged atoms : 2644 net assigned charge : 3.140012 assigned positive charge : 419.0147 centred at (gu) : 90.41016 90.36327 91.69367 assigned negative charge : -415.8753 centred at (gu) : 90.16896 90.19597 91.62331 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7883 nv = 96 ne = 84 npr = 56847 no. pairs analyzed = 56847 no. exposed pairs = 3344 no. arc points = 23513 no. surface atoms = 1125 nbur = 1672 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 4518 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.4200000 number of dielectric boundary points 3751 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2353 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9315 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5288663E-09 2.1111955E-08 midg,1,midg; midg,igrid,midg -1.7738671E-08 3.0271796E-08 1,midg,midg; igrid,midg,midg -2.7527884E-08 4.1482394E-08 gauss-seidel spectral radius is 0.9875454 estimated iterations to convergence 73 setup time was (sec) 0.7000000 now iterating at: 03:47:21 rms-change max change #iterations 0.1541924 20.23132 at 10iterations 1.5907940E-02 2.061956 at 20iterations 1.6587531E-03 0.1966705 at 30iterations 1.9719866E-04 2.8491974E-02 at 40iterations 3.5332669E-05 4.5795441E-03 at 50iterations finished qdiffx linear iterations at : 03:47:24 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 3.5332669E-05 4.5795441E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 03:47:26 4.067u 0.157s 0:05.18 81.2% 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 Tue Oct 11 2011 at 03:47:26 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2797 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.933697 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): -12.19300 37.01100 ymin,ymax (A): -26.78500 21.73600 zmin,zma (A): -9.647000 45.58400 x,y,z range (A): 49.20400 48.52100 55.23100 scale (grids/A): 1.933697 object centre (A): 12.40900 -2.524500 17.96850 number of atom coordinates read : 2797 total number of charged atoms : 2644 net assigned charge : 3.140012 assigned positive charge : 419.0147 centred at (gu) : 91.22995 91.08924 95.08027 assigned negative charge : -415.8753 centred at (gu) : 90.50668 90.58774 94.86979 start vw surface at 0.2000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 84662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23513 grid for indexing accessible points = 1.400000 m= 32620 mr = 60217 m= 5440 mr = 24695 m= 297 mr = 3471 m= 0 mr = 97 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1759 time to turn everything in is 0.8000000 number of dielectric boundary points 34539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 182 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 20835 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) : 0.6445656 object centre at (A) : 12.40900 -2.524500 17.96850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0902585E-02 7.4218772E-03 midg,1,midg; midg,igrid,midg -1.0634662E-02 3.0507077E-02 1,midg,midg; igrid,midg,midg -1.2586924E-02 6.3174352E-02 gauss-seidel spectral radius is 0.9986960 estimated iterations to convergence 219 setup time was (sec) 1.170000 now iterating at: 03:47:27 rms-change max change #iterations 4.514179 193.7219 at 10iterations 2.153805 70.00451 at 20iterations 1.029346 34.28106 at 30iterations 0.4917296 16.48042 at 40iterations 0.2346131 7.176911 at 50iterations 0.1123050 3.254185 at 60iterations 5.3646866E-02 1.566673 at 70iterations 2.5607010E-02 0.7433090 at 80iterations 1.2214001E-02 0.3397913 at 90iterations 5.8145872E-03 0.1699867 at 100iterations 2.7804568E-03 9.7333908E-02 at 110iterations 1.3316775E-03 3.9994240E-02 at 120iterations finished qdiffx linear iterations at : 03:47:36 total time elapsed so far: 9.740000 # loops : 120 mean,max change (kT/e) : 1.3316775E-03 3.9994240E-02 energy calculations done at 9.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.970000 DelPhi exited at 03:47:36 9.971u 0.274s 0:10.54 97.1% 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 03:47:36 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2797 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.900545 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): -12.19300 37.01100 ymin,ymax (A): -26.78500 21.73600 zmin,zma (A): -9.647000 45.58400 x,y,z range (A): 49.20400 48.52100 55.23100 scale (grids/A): 2.900545 object centre (A): 12.40900 -2.524500 17.96850 number of atom coordinates read : 2797 total number of charged atoms : 2644 net assigned charge : 3.140012 assigned positive charge : 419.0147 centred at (gu) : 91.84473 91.63373 97.62014 assigned negative charge : -415.8753 centred at (gu) : 90.75993 90.88149 97.30456 start vw surface at 0.1900000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 195366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23513 grid for indexing accessible points = 1.400000 m= 104114 mr = 145097 m= 39715 mr = 86723 m= 9763 mr = 32587 m= 1313 mr = 7338 m= 61 mr = 896 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 6304 time to turn everything in is 2.020000 number of dielectric boundary points 77668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 21144 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) : 1.933697 object centre at (A) : 12.40900 -2.524500 17.96850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4905042 0.2873645 midg,1,midg; midg,igrid,midg -0.1156122 0.3671995 1,midg,midg; igrid,midg,midg -9.2136830E-02 0.5261198 gauss-seidel spectral radius is 0.9992725 estimated iterations to convergence 293 setup time was (sec) 2.440000 now iterating at: 03:47:39 rms-change max change #iterations 10.42577 377.7911 at 10iterations 6.110686 127.9033 at 20iterations 3.568609 68.16650 at 30iterations 2.080415 36.16319 at 40iterations 1.208989 22.34044 at 50iterations 0.7037553 13.54832 at 60iterations 0.4084648 7.040465 at 70iterations 0.2365992 4.718534 at 80iterations 0.1373633 2.465906 at 90iterations 7.9692699E-02 1.328099 at 100iterations 4.6166025E-02 0.8378792 at 110iterations 2.6756963E-02 0.4457293 at 120iterations 1.5485276E-02 0.2484398 at 130iterations 8.9826612E-03 0.1507597 at 140iterations 5.2269865E-03 0.1009073 at 150iterations 3.0462337E-03 4.9743652E-02 at 160iterations 1.7935104E-03 3.4610271E-02 at 170iterations 1.0698042E-03 1.9386292E-02 at 180iterations finished qdiffx linear iterations at : 03:47:53 total time elapsed so far: 16.27000 # loops : 180 mean,max change (kT/e) : 1.0698042E-03 1.9386292E-02 energy calculations done at 16.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.50000 DelPhi exited at 03:47:53 16.504u 0.284s 0:17.10 98.1% 0+0k 0+0io 0pf+0w