Mon Oct 10 09:45:30 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 Mon Oct 10 2011 at 09:45:30 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 = 2908 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5669061 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): 111.9540 174.7510 ymin,ymax (A): -42.41200 10.67500 zmin,zma (A): 49.90700 104.9130 x,y,z range (A): 62.79700 53.08700 55.00600 scale (grids/A): 0.5669061 object centre (A): 143.3525 -15.86850 77.41000 number of atom coordinates read : 2908 total number of charged atoms : 2759 net assigned charge : 8.000018 assigned positive charge : 427.0938 centred at (gu) : 90.32372 88.77332 88.59019 assigned negative charge : -419.0944 centred at (gu) : 90.33772 88.88072 88.46878 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6166 nv = 96 ne = 84 npr = 56248 no. pairs analyzed = 56248 no. exposed pairs = 4637 no. arc points = 33762 no. surface atoms = 1526 nbur = 1382 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 335 mr = 2438 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3300 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.7917928E-10 1.9256086E-09 midg,1,midg; midg,igrid,midg 3.3652598E-09 -2.4209584E-10 1,midg,midg; igrid,midg,midg 1.1932894E-09 9.8597785E-10 gauss-seidel spectral radius is 0.9839621 estimated iterations to convergence 65 setup time was (sec) 0.6300000 now iterating at: 09:45:31 rms-change max change #iterations 8.4758170E-02 15.91201 at 10iterations 6.2002111E-03 0.9295654 at 20iterations 4.6870828E-04 7.5160027E-02 at 30iterations 4.8606777E-05 6.7005157E-03 at 40iterations 9.0894482E-06 1.0356903E-03 at 50iterations finished qdiffx linear iterations at : 09:45:34 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 9.0894482E-06 1.0356903E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 09:45:35 4.091u 0.274s 0:05.02 86.8% 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 Mon Oct 10 2011 at 09:45:35 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 = 2908 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.700718 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): 111.9540 174.7510 ymin,ymax (A): -42.41200 10.67500 zmin,zma (A): 49.90700 104.9130 x,y,z range (A): 62.79700 53.08700 55.00600 scale (grids/A): 1.700718 object centre (A): 143.3525 -15.86850 77.41000 number of atom coordinates read : 2908 total number of charged atoms : 2759 net assigned charge : 8.000018 assigned positive charge : 427.0938 centred at (gu) : 90.97062 86.31962 85.77003 assigned negative charge : -419.0944 centred at (gu) : 91.01289 86.64197 85.40626 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 65520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33762 grid for indexing accessible points = 1.400000 m= 19621 mr = 37691 m= 2603 mr = 11377 m= 112 mr = 1056 m= 3 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 37730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 292 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21339 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) : 0.5669061 object centre at (A) : 143.3525 -15.86850 77.41000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0099528E-03 1.9564303E-02 midg,1,midg; midg,igrid,midg 2.0936461E-02 5.5768988E-03 1,midg,midg; igrid,midg,midg 9.8414645E-03 1.5116986E-02 gauss-seidel spectral radius is 0.9983552 estimated iterations to convergence 196 setup time was (sec) 0.9200000 now iterating at: 09:45:36 rms-change max change #iterations 3.518760 159.6712 at 10iterations 1.520908 55.13028 at 20iterations 0.6571605 27.10423 at 30iterations 0.2839527 12.03917 at 40iterations 0.1230185 4.421389 at 50iterations 5.3479895E-02 2.117023 at 60iterations 2.3047835E-02 0.8615456 at 70iterations 1.0022656E-02 0.3640819 at 80iterations 4.3537221E-03 0.1697922 at 90iterations 1.8810716E-03 7.0575714E-02 at 100iterations 8.2101696E-04 3.0289650E-02 at 110iterations 3.5455934E-04 1.3953209E-02 at 120iterations finished qdiffx linear iterations at : 09:45:44 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 3.5455934E-04 1.3953209E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.380000 DelPhi exited at 09:45:45 9.381u 0.307s 0:09.96 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 Mon Oct 10 2011 at 09:45:45 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 = 2908 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.551077 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): 111.9540 174.7510 ymin,ymax (A): -42.41200 10.67500 zmin,zma (A): 49.90700 104.9130 x,y,z range (A): 62.79700 53.08700 55.00600 scale (grids/A): 2.551077 object centre (A): 143.3525 -15.86850 77.41000 number of atom coordinates read : 2908 total number of charged atoms : 2759 net assigned charge : 8.000018 assigned positive charge : 427.0938 centred at (gu) : 91.45590 84.47928 83.65498 assigned negative charge : -419.0944 centred at (gu) : 91.51927 84.96297 83.10928 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 151294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33762 grid for indexing accessible points = 1.400000 m= 64346 mr = 94051 m= 20192 mr = 45269 m= 4027 mr = 13357 m= 389 mr = 2280 m= 8 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.510000 number of dielectric boundary points 85167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 22064 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) : 1.700718 object centre at (A) : 143.3525 -15.86850 77.41000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1435728 0.2694917 midg,1,midg; midg,igrid,midg 0.2558040 0.1128055 1,midg,midg; igrid,midg,midg 0.1397587 0.2499974 gauss-seidel spectral radius is 0.9992147 estimated iterations to convergence 282 setup time was (sec) 1.840000 now iterating at: 09:45:47 rms-change max change #iterations 9.294014 323.1583 at 10iterations 5.533652 174.0441 at 20iterations 3.233184 80.82953 at 30iterations 1.876822 42.72794 at 40iterations 1.081380 27.11468 at 50iterations 0.6204486 16.23929 at 60iterations 0.3549663 8.926182 at 70iterations 0.2022915 5.048846 at 80iterations 0.1149736 2.838499 at 90iterations 6.5493092E-02 1.662665 at 100iterations 3.7091643E-02 0.9037257 at 110iterations 2.0998007E-02 0.4417915 at 120iterations 1.1893172E-02 0.2487289 at 130iterations 6.7257546E-03 0.1436385 at 140iterations 3.8038942E-03 8.3089828E-02 at 150iterations 2.1490895E-03 4.4075966E-02 at 160iterations 1.2153707E-03 2.7565479E-02 at 170iterations 6.8629521E-04 1.4038086E-02 at 180iterations finished qdiffx linear iterations at : 09:46:01 total time elapsed so far: 15.53000 # loops : 180 mean,max change (kT/e) : 6.8629521E-04 1.4038086E-02 energy calculations done at 15.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.70000 DelPhi exited at 09:46:01 15.704u 0.314s 0:16.31 98.1% 0+0k 0+0io 0pf+0w