Mon Oct 10 14:02:08 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 Mon Oct 10 2011 at 14:02:08 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2116 !!! WARNING: HIR 224 has a net charge of 0.5140 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: 0.6342533 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): 69.57500 125.7040 ymin,ymax (A): -8.046000 37.55700 zmin,zma (A): 3.446000 52.13800 x,y,z range (A): 56.12900 45.60300 48.69200 scale (grids/A): 0.6342533 object centre (A): 97.63950 14.75550 27.79200 number of atom coordinates read : 2116 total number of charged atoms : 2048 net assigned charge : -0.4859697 assigned positive charge : 317.7246 centred at (gu) : 90.42444 88.98396 88.97956 assigned negative charge : -318.2114 centred at (gu) : 90.47053 89.06358 89.08230 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5808 nv = 96 ne = 84 npr = 41260 no. pairs analyzed = 41260 no. exposed pairs = 2998 no. arc points = 20547 no. surface atoms = 1002 nbur = 1114 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 339 mr = 2927 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.1700000 number of dielectric boundary points 3175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1989 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.4602894E-09 -7.3761188E-09 midg,1,midg; midg,igrid,midg 7.1381288E-09 -5.8434217E-09 1,midg,midg; igrid,midg,midg 2.7274465E-09 -4.9596682E-09 gauss-seidel spectral radius is 0.9870893 estimated iterations to convergence 72 setup time was (sec) 0.3500000 now iterating at: 14:02:08 rms-change max change #iterations 0.1266614 20.45223 at 10iterations 1.2198576E-02 1.948629 at 20iterations 1.1735909E-03 0.2123408 at 30iterations 1.1349948E-04 1.8746376E-02 at 40iterations 1.1156997E-05 1.5926361E-03 at 50iterations finished qdiffx linear iterations at : 14:02:11 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.1156997E-05 1.5926361E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:02:12 3.357u 0.191s 0:04.63 76.4% 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 14:02:12 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2116 !!! WARNING: HIR 224 has a net charge of 0.5140 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: 1.902760 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): 69.57500 125.7040 ymin,ymax (A): -8.046000 37.55700 zmin,zma (A): 3.446000 52.13800 x,y,z range (A): 56.12900 45.60300 48.69200 scale (grids/A): 1.902760 object centre (A): 97.63950 14.75550 27.79200 number of atom coordinates read : 2116 total number of charged atoms : 2048 net assigned charge : -0.4859697 assigned positive charge : 317.7246 centred at (gu) : 91.27315 86.95162 86.93843 assigned negative charge : -318.2114 centred at (gu) : 91.41195 87.19085 87.24707 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61985 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20547 grid for indexing accessible points = 1.400000 m= 22376 mr = 40776 m= 3980 mr = 15882 m= 291 mr = 2544 m= 5 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 297 time to turn everything in is 0.3200000 number of dielectric boundary points 29310 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 16134 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) : 0.6342533 object centre at (A) : 97.63950 14.75550 27.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1587992E-02 7.9132896E-03 midg,1,midg; midg,igrid,midg 9.2229443E-03 -6.9430312E-03 1,midg,midg; igrid,midg,midg -3.5518523E-02 -1.6521936E-02 gauss-seidel spectral radius is 0.9985937 estimated iterations to convergence 211 setup time was (sec) 0.5500000 now iterating at: 14:02:13 rms-change max change #iterations 3.807314 162.9814 at 10iterations 1.756205 65.08648 at 20iterations 0.8153668 29.95031 at 30iterations 0.3766785 13.24077 at 40iterations 0.1743860 6.093842 at 50iterations 8.0886804E-02 2.756680 at 60iterations 3.7384696E-02 1.249851 at 70iterations 1.7338512E-02 0.5959558 at 80iterations 8.0365138E-03 0.2763738 at 90iterations 3.7246607E-03 0.1221859 at 100iterations 1.7239721E-03 6.3834429E-02 at 110iterations 8.0198317E-04 2.5947571E-02 at 120iterations finished qdiffx linear iterations at : 14:02:20 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 8.0198317E-04 2.5947571E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 14:02:21 7.739u 0.180s 0:08.62 91.7% 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 Mon Oct 10 2011 at 14:02:21 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2116 !!! WARNING: HIR 224 has a net charge of 0.5140 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: 2.854140 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): 69.57500 125.7040 ymin,ymax (A): -8.046000 37.55700 zmin,zma (A): 3.446000 52.13800 x,y,z range (A): 56.12900 45.60300 48.69200 scale (grids/A): 2.854140 object centre (A): 97.63950 14.75550 27.79200 number of atom coordinates read : 2116 total number of charged atoms : 2048 net assigned charge : -0.4859697 assigned positive charge : 317.7246 centred at (gu) : 91.90967 85.42732 85.40769 assigned negative charge : -318.2114 centred at (gu) : 92.11798 85.78627 85.87072 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 143223 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20547 grid for indexing accessible points = 1.400000 m= 70226 mr = 99361 m= 27254 mr = 55709 m= 7291 mr = 21559 m= 1243 mr = 5591 m= 89 mr = 908 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1039 time to turn everything in is 0.8200000 number of dielectric boundary points 66149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 16384 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) : 1.902760 object centre at (A) : 97.63950 14.75550 27.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3205407 0.1165071 midg,1,midg; midg,igrid,midg 0.1268568 -4.9854495E-02 1,midg,midg; igrid,midg,midg -0.7258160 -0.2253630 gauss-seidel spectral radius is 0.9992476 estimated iterations to convergence 288 setup time was (sec) 1.060000 now iterating at: 14:02:22 rms-change max change #iterations 9.018154 395.8069 at 10iterations 5.251192 126.4965 at 20iterations 3.033327 66.74335 at 30iterations 1.748469 36.55900 at 40iterations 1.007464 20.55212 at 50iterations 0.5793300 12.29302 at 60iterations 0.3326291 6.692410 at 70iterations 0.1906917 4.028195 at 80iterations 0.1092135 2.342817 at 90iterations 6.2559292E-02 1.266040 at 100iterations 3.5860077E-02 0.7101746 at 110iterations 2.0479932E-02 0.4685993 at 120iterations 1.1739836E-02 0.2363749 at 130iterations 6.7055519E-03 0.1352234 at 140iterations 3.8348723E-03 7.1848869E-02 at 150iterations 2.1965536E-03 4.6509743E-02 at 160iterations 1.2528804E-03 2.4749756E-02 at 170iterations 7.1690360E-04 1.4722824E-02 at 180iterations finished qdiffx linear iterations at : 14:02:34 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 7.1690360E-04 1.4722824E-02 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 14:02:34 12.340u 0.202s 0:13.06 96.0% 0+0k 0+0io 0pf+0w