Sun Oct 9 02:43:11 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 Sun Oct 9 2011 at 02:43:11 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 = 2172 !!! WARNING: MG3 319 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6870598 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): 0.5979999 41.47400 ymin,ymax (A): -24.43300 18.05200 zmin,zma (A): -32.82100 18.99400 x,y,z range (A): 40.87600 42.48500 51.81500 scale (grids/A): 0.6870598 object centre (A): 21.03600 -3.190500 -6.913500 number of atom coordinates read : 2172 total number of charged atoms : 2040 net assigned charge : -2.599991 assigned positive charge : 324.9067 centred at (gu) : 89.64413 90.23594 90.32843 assigned negative charge : -327.5070 centred at (gu) : 89.64065 90.21921 90.32385 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6897 nv = 96 ne = 84 npr = 46316 no. pairs analyzed = 46316 no. exposed pairs = 2407 no. arc points = 16796 no. surface atoms = 821 nbur = 1351 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 4155 m= 0 mr = 102 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 304 time to turn everything in is 0.1700000 number of dielectric boundary points 3070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1583 ## 131 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7786 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3952314E-08 -1.2668115E-08 midg,1,midg; midg,igrid,midg -1.7977754E-08 -8.3054887E-09 1,midg,midg; igrid,midg,midg -1.5552194E-08 -1.1442562E-08 gauss-seidel spectral radius is 0.9889701 estimated iterations to convergence 78 setup time was (sec) 0.3600000 now iterating at: 02:43:11 rms-change max change #iterations 0.1837311 27.29234 at 10iterations 2.1598339E-02 3.080103 at 20iterations 2.4823772E-03 0.3791351 at 30iterations 2.9219809E-04 4.2380333E-02 at 40iterations 3.3572953E-05 5.5599213E-03 at 50iterations finished qdiffx linear iterations at : 02:43:14 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 3.3572953E-05 5.5599213E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 02:43:15 3.334u 0.164s 0:03.81 91.6% 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 Sun Oct 9 2011 at 02:43:15 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 = 2172 !!! WARNING: MG3 319 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.061179 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): 0.5979999 41.47400 ymin,ymax (A): -24.43300 18.05200 zmin,zma (A): -32.82100 18.99400 x,y,z range (A): 40.87600 42.48500 51.81500 scale (grids/A): 2.061179 object centre (A): 21.03600 -3.190500 -6.913500 number of atom coordinates read : 2172 total number of charged atoms : 2040 net assigned charge : -2.599991 assigned positive charge : 324.9067 centred at (gu) : 88.93216 90.70781 90.98485 assigned negative charge : -327.5070 centred at (gu) : 88.92202 90.65749 90.97158 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16796 grid for indexing accessible points = 1.400000 m= 29128 mr = 53295 m= 5639 mr = 22849 m= 504 mr = 4194 m= 7 mr = 325 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 8075 time to turn everything in is 0.3600000 number of dielectric boundary points 28199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 16171 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) : 0.6870598 object centre at (A) : 21.03600 -3.190500 -6.913500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2045373E-04 -3.1273020E-04 midg,1,midg; midg,igrid,midg 1.6392142E-03 -1.3216164E-02 1,midg,midg; igrid,midg,midg -9.3486654E-03 -4.4853380E-03 gauss-seidel spectral radius is 0.9987701 estimated iterations to convergence 226 setup time was (sec) 0.5700000 now iterating at: 02:43:15 rms-change max change #iterations 4.448278 181.9456 at 10iterations 2.166330 79.04324 at 20iterations 1.054223 34.94138 at 30iterations 0.5158184 15.26173 at 40iterations 0.2510329 8.064339 at 50iterations 0.1229759 4.378811 at 60iterations 5.9686035E-02 1.875704 at 70iterations 2.9093288E-02 0.9085231 at 80iterations 1.4134569E-02 0.4458771 at 90iterations 6.8876436E-03 0.1973953 at 100iterations 3.3697505E-03 0.1083980 at 110iterations 1.6408094E-03 5.2395821E-02 at 120iterations finished qdiffx linear iterations at : 02:43:23 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.6408094E-03 5.2395821E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 02:43:23 7.867u 0.205s 0:08.39 96.0% 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 Sun Oct 9 2011 at 02:43:23 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 = 2172 !!! WARNING: MG3 319 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.091769 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): 0.5979999 41.47400 ymin,ymax (A): -24.43300 18.05200 zmin,zma (A): -32.82100 18.99400 x,y,z range (A): 40.87600 42.48500 51.81500 scale (grids/A): 3.091769 object centre (A): 21.03600 -3.190500 -6.913500 number of atom coordinates read : 2172 total number of charged atoms : 2040 net assigned charge : -2.599991 assigned positive charge : 324.9067 centred at (gu) : 88.39812 91.06170 91.47729 assigned negative charge : -327.5070 centred at (gu) : 88.38300 90.98636 91.45750 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 169915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16796 grid for indexing accessible points = 1.400000 m= 91014 mr = 127861 m= 37194 mr = 77150 m= 10842 mr = 31768 m= 2270 mr = 9057 m= 287 mr = 1923 m= 7 mr = 208 m= 0 mr = 3 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 27598 time to turn everything in is 1.070000 number of dielectric boundary points 63559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 16320 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) : 2.061179 object centre at (A) : 21.03600 -3.190500 -6.913500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5961097E-02 0.1380511 midg,1,midg; midg,igrid,midg 0.1011908 -0.1876357 1,midg,midg; igrid,midg,midg -3.9379146E-02 -0.1038465 gauss-seidel spectral radius is 0.9992727 estimated iterations to convergence 293 setup time was (sec) 1.300000 now iterating at: 02:43:25 rms-change max change #iterations 9.931507 398.1010 at 10iterations 5.723344 103.8918 at 20iterations 3.299379 65.08444 at 30iterations 1.901038 33.71550 at 40iterations 1.095044 23.68240 at 50iterations 0.6319801 11.11428 at 60iterations 0.3638346 6.482200 at 70iterations 0.2101424 3.601271 at 80iterations 0.1212384 2.168636 at 90iterations 6.9798745E-02 1.254335 at 100iterations 4.0247343E-02 0.6638794 at 110iterations 2.3148315E-02 0.4148598 at 120iterations 1.3363292E-02 0.2343740 at 130iterations 7.7198842E-03 0.1340769 at 140iterations 4.4527892E-03 7.9820633E-02 at 150iterations 2.5698934E-03 4.5402527E-02 at 160iterations 1.4817676E-03 2.5303483E-02 at 170iterations 8.5511571E-04 1.4629364E-02 at 180iterations finished qdiffx linear iterations at : 02:43:36 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 8.5511571E-04 1.4629364E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 02:43:36 12.477u 0.206s 0:13.01 97.3% 0+0k 0+0io 0pf+0w