Sat Oct 8 20:51:29 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 Sat Oct 8 2011 at 20:51:29 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 = 2579 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: 0.6214433 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): -32.29200 17.50500 ymin,ymax (A): -23.63000 22.27900 zmin,zma (A): -12.62000 44.66600 x,y,z range (A): 49.79700 45.90900 57.28600 scale (grids/A): 0.6214433 object centre (A): -7.393500 -0.6754999 16.02300 number of atom coordinates read : 2579 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 88.70187 89.37057 89.77026 assigned negative charge : -386.5045 centred at (gu) : 88.59425 89.41097 89.68080 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6424 nv = 96 ne = 84 npr = 54348 no. pairs analyzed = 54348 no. exposed pairs = 2934 no. arc points = 20959 no. surface atoms = 990 nbur = 1589 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3610 m= 0 mr = 26 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 93 time to turn everything in is 0.3100000 number of dielectric boundary points 3108 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2157 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8092 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3491616E-09 8.6999128E-09 midg,1,midg; midg,igrid,midg 6.6805712E-09 2.4147562E-10 1,midg,midg; igrid,midg,midg -6.0314034E-09 7.8076168E-09 gauss-seidel spectral radius is 0.9865816 estimated iterations to convergence 71 setup time was (sec) 0.6100000 now iterating at: 20:51:30 rms-change max change #iterations 0.1243506 20.38819 at 10iterations 1.1492456E-02 1.610688 at 20iterations 1.0635349E-03 0.1617126 at 30iterations 9.7792421E-05 1.6777039E-02 at 40iterations 9.2315822E-06 1.3732910E-03 at 50iterations finished qdiffx linear iterations at : 20:51:34 total time elapsed so far: 4.520000 # loops : 50 mean,max change (kT/e) : 9.2315822E-06 1.3732910E-03 energy calculations done at 4.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 20:51:34 4.687u 0.398s 0:05.41 93.7% 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 Sat Oct 8 2011 at 20:51:35 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 = 2579 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: 1.864330 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): -32.29200 17.50500 ymin,ymax (A): -23.63000 22.27900 zmin,zma (A): -12.62000 44.66600 x,y,z range (A): 49.79700 45.90900 57.28600 scale (grids/A): 1.864330 object centre (A): -7.393500 -0.6754999 16.02300 number of atom coordinates read : 2579 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 86.10521 88.11129 89.31002 assigned negative charge : -386.5045 centred at (gu) : 85.78232 88.23267 89.04211 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20959 grid for indexing accessible points = 1.400000 m= 23507 mr = 49023 m= 3109 mr = 17123 m= 136 mr = 1855 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 3712 time to turn everything in is 0.5700000 number of dielectric boundary points 28604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19246 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) : 0.6214433 object centre at (A) : -7.393500 -0.6754999 16.02300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3009734E-02 1.8926604E-02 midg,1,midg; midg,igrid,midg 1.1333062E-02 3.7461387E-03 1,midg,midg; igrid,midg,midg -9.9162282E-03 3.3846658E-02 gauss-seidel spectral radius is 0.9985690 estimated iterations to convergence 210 setup time was (sec) 0.8700000 now iterating at: 20:51:36 rms-change max change #iterations 4.012637 170.6164 at 10iterations 1.851553 69.39387 at 20iterations 0.8500038 27.93051 at 30iterations 0.3912120 12.84653 at 40iterations 0.1806964 6.080963 at 50iterations 8.2876384E-02 3.004061 at 60iterations 3.8334414E-02 1.328579 at 70iterations 1.7548596E-02 0.5256805 at 80iterations 8.1077525E-03 0.2630024 at 90iterations 3.7298065E-03 0.1255569 at 100iterations 1.7150507E-03 6.0880661E-02 at 110iterations 7.8979880E-04 2.7228117E-02 at 120iterations finished qdiffx linear iterations at : 20:51:46 total time elapsed so far: 10.72000 # loops : 120 mean,max change (kT/e) : 7.8979880E-04 2.7228117E-02 energy calculations done at 10.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.88000 DelPhi exited at 20:51:46 10.888u 0.429s 0:11.61 97.3% 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 Sat Oct 8 2011 at 20:51:46 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 = 2579 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: 2.796495 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): -32.29200 17.50500 ymin,ymax (A): -23.63000 22.27900 zmin,zma (A): -12.62000 44.66600 x,y,z range (A): 49.79700 45.90900 57.28600 scale (grids/A): 2.796495 object centre (A): -7.393500 -0.6754999 16.02300 number of atom coordinates read : 2579 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 84.15776 87.16673 88.96488 assigned negative charge : -386.5045 centred at (gu) : 83.67343 87.34895 88.56310 start vw surface at 0.1100000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 162129 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20959 grid for indexing accessible points = 1.400000 m= 78491 mr = 118549 m= 25420 mr = 64436 m= 5309 mr = 20180 m= 587 mr = 3870 m= 25 mr = 368 m= 0 mr = 11 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 12318 time to turn everything in is 1.420000 number of dielectric boundary points 64547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 19622 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) : 1.864330 object centre at (A) : -7.393500 -0.6754999 16.02300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1069125 0.1872616 midg,1,midg; midg,igrid,midg 0.1356163 1.9259388E-02 1,midg,midg; igrid,midg,midg -7.4661724E-02 0.4569047 gauss-seidel spectral radius is 0.9992329 estimated iterations to convergence 285 setup time was (sec) 1.740000 now iterating at: 20:51:48 rms-change max change #iterations 9.438243 309.5499 at 10iterations 5.409204 114.3785 at 20iterations 3.091633 74.00822 at 30iterations 1.761217 33.73750 at 40iterations 1.003774 18.78950 at 50iterations 0.5703981 13.15173 at 60iterations 0.3253058 6.148201 at 70iterations 0.1846049 3.488735 at 80iterations 0.1050373 2.234682 at 90iterations 5.9759431E-02 1.147350 at 100iterations 3.3896282E-02 0.6800213 at 110iterations 1.9322801E-02 0.3518867 at 120iterations 1.0976323E-02 0.2149162 at 130iterations 6.2325485E-03 0.1163845 at 140iterations 3.5427511E-03 6.7679882E-02 at 150iterations 2.0143415E-03 3.7839890E-02 at 160iterations 1.1472646E-03 2.1297455E-02 at 170iterations 6.5073895E-04 1.3726950E-02 at 180iterations finished qdiffx linear iterations at : 20:52:04 total time elapsed so far: 17.52000 # loops : 180 mean,max change (kT/e) : 6.5073895E-04 1.3726950E-02 energy calculations done at 17.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.67000 DelPhi exited at 20:52:05 17.677u 0.477s 0:18.42 98.4% 0+0k 0+0io 0pf+0w