Tue Oct 11 07:32:16 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 Tue Oct 11 2011 at 07:32:16 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 !!! WARNING: SEP 54 has a net charge of -0.4750 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: 0.5990241 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): 0.3270000 48.89600 ymin,ymax (A): -7.322000 49.11300 zmin,zma (A): 1.312000 60.74200 x,y,z range (A): 48.56900 56.43500 59.43000 scale (grids/A): 0.5990241 object centre (A): 24.61150 20.89550 31.02700 number of atom coordinates read : 3239 total number of charged atoms : 3094 net assigned charge : -1.474988 assigned positive charge : 488.9798 centred at (gu) : 89.76797 89.00468 90.89458 assigned negative charge : -490.4559 centred at (gu) : 89.69865 88.92156 90.84125 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7713 nv = 96 ne = 84 npr = 66546 no. pairs analyzed = 66546 no. exposed pairs = 3662 no. arc points = 25541 no. surface atoms = 1245 nbur = 1994 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 4590 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 79 time to turn everything in is 0.4200000 number of dielectric boundary points 3474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2598 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9713 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4294884E-09 2.2067115E-09 midg,1,midg; midg,igrid,midg -5.4526437E-09 2.4553826E-09 1,midg,midg; igrid,midg,midg -3.9065204E-09 2.3575373E-09 gauss-seidel spectral radius is 0.9856259 estimated iterations to convergence 68 setup time was (sec) 0.7000000 now iterating at: 07:32:17 rms-change max change #iterations 0.1215232 16.44637 at 10iterations 1.0858721E-02 1.285213 at 20iterations 1.0305312E-03 0.1676464 at 30iterations 1.4934460E-04 2.7545929E-02 at 40iterations 2.9076034E-05 5.9146881E-03 at 50iterations finished qdiffx linear iterations at : 07:32:20 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 2.9076034E-05 5.9146881E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 07:32:21 4.232u 0.254s 0:05.23 85.6% 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 07:32:21 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 !!! WARNING: SEP 54 has a net charge of -0.4750 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: 1.797072 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): 0.3270000 48.89600 ymin,ymax (A): -7.322000 49.11300 zmin,zma (A): 1.312000 60.74200 x,y,z range (A): 48.56900 56.43500 59.43000 scale (grids/A): 1.797072 object centre (A): 24.61150 20.89550 31.02700 number of atom coordinates read : 3239 total number of charged atoms : 3094 net assigned charge : -1.474988 assigned positive charge : 488.9798 centred at (gu) : 89.30321 87.01352 92.68288 assigned negative charge : -490.4559 centred at (gu) : 89.09538 86.76437 92.52345 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 84540 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25541 grid for indexing accessible points = 1.400000 m= 31409 mr = 61343 m= 4521 mr = 24165 m= 166 mr = 2904 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 2543 time to turn everything in is 0.7400000 number of dielectric boundary points 32177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 24142 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) : 0.5990241 object centre at (A) : 24.61150 20.89550 31.02700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0270239E-02 3.5505565E-03 midg,1,midg; midg,igrid,midg -2.1779357E-02 6.8858447E-03 1,midg,midg; igrid,midg,midg -1.5249447E-02 4.0002237E-03 gauss-seidel spectral radius is 0.9985301 estimated iterations to convergence 207 setup time was (sec) 1.040000 now iterating at: 07:32:23 rms-change max change #iterations 4.325645 178.0001 at 10iterations 1.971987 69.62629 at 20iterations 0.8978488 27.50750 at 30iterations 0.4099051 11.93537 at 40iterations 0.1869999 6.266068 at 50iterations 8.5638307E-02 2.608383 at 60iterations 3.8872186E-02 1.125879 at 70iterations 1.7848697E-02 0.5418701 at 80iterations 8.1808716E-03 0.2518201 at 90iterations 3.7485054E-03 0.1203957 at 100iterations 1.7361345E-03 5.5622101E-02 at 110iterations 8.0513378E-04 2.6794434E-02 at 120iterations finished qdiffx linear iterations at : 07:32:31 total time elapsed so far: 9.560000 # loops : 120 mean,max change (kT/e) : 8.0513378E-04 2.6794434E-02 energy calculations done at 9.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.740000 DelPhi exited at 07:32:32 9.741u 0.322s 0:10.60 94.9% 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 07:32:32 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 !!! WARNING: SEP 54 has a net charge of -0.4750 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: 2.695608 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): 0.3270000 48.89600 ymin,ymax (A): -7.322000 49.11300 zmin,zma (A): 1.312000 60.74200 x,y,z range (A): 48.56900 56.43500 59.43000 scale (grids/A): 2.695608 object centre (A): 24.61150 20.89550 31.02700 number of atom coordinates read : 3239 total number of charged atoms : 3094 net assigned charge : -1.474988 assigned positive charge : 488.9798 centred at (gu) : 88.95454 85.52008 94.02401 assigned negative charge : -490.4559 centred at (gu) : 88.64288 85.14626 93.78506 start vw surface at 0.1800000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 195919 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25541 grid for indexing accessible points = 1.400000 m= 103168 mr = 147937 m= 36503 mr = 87096 m= 7919 mr = 30109 m= 814 mr = 6084 m= 27 mr = 507 m= 0 mr = 10 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 8755 time to turn everything in is 1.890000 number of dielectric boundary points 72607 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 24745 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) : 1.797072 object centre at (A) : 24.61150 20.89550 31.02700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3174460 -0.2028930 midg,1,midg; midg,igrid,midg -0.3368937 2.7004015E-02 1,midg,midg; igrid,midg,midg -0.1979745 2.9047571E-02 gauss-seidel spectral radius is 0.9992373 estimated iterations to convergence 286 setup time was (sec) 2.230000 now iterating at: 07:32:35 rms-change max change #iterations 10.31517 356.5723 at 10iterations 5.941296 113.6219 at 20iterations 3.408803 72.05347 at 30iterations 1.944270 39.48211 at 40iterations 1.112230 19.96001 at 50iterations 0.6362768 11.05863 at 60iterations 0.3626337 6.082386 at 70iterations 0.2066294 3.704312 at 80iterations 0.1177661 2.172928 at 90iterations 6.7189381E-02 1.114616 at 100iterations 3.8279381E-02 0.6729765 at 110iterations 2.1799853E-02 0.3783073 at 120iterations 1.2433626E-02 0.2270079 at 130iterations 7.0821219E-03 0.1266975 at 140iterations 4.0406385E-03 7.1491241E-02 at 150iterations 2.3094991E-03 3.9745331E-02 at 160iterations 1.3233261E-03 2.3180008E-02 at 170iterations 7.6121552E-04 1.4400482E-02 at 180iterations finished qdiffx linear iterations at : 07:32:49 total time elapsed so far: 16.39000 # loops : 180 mean,max change (kT/e) : 7.6121552E-04 1.4400482E-02 energy calculations done at 16.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.56000 DelPhi exited at 07:32:49 16.564u 0.325s 0:17.17 98.3% 0+0k 0+0io 0pf+0w