Sat Oct 8 15:10:44 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 15:10:44 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2431 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5963948 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): 13.10300 72.79500 ymin,ymax (A): -13.31000 32.73600 zmin,zma (A): -3.179000 51.67100 x,y,z range (A): 59.69200 46.04600 54.85000 scale (grids/A): 0.5963948 object centre (A): 42.94900 9.712999 24.24600 number of atom coordinates read : 2431 total number of charged atoms : 2355 net assigned charge : 8.500020 assigned positive charge : 369.5671 centred at (gu) : 90.53458 89.08495 90.37103 assigned negative charge : -361.0677 centred at (gu) : 90.44174 88.99656 90.52679 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6016 nv = 96 ne = 84 npr = 45536 no. pairs analyzed = 45536 no. exposed pairs = 3421 no. arc points = 24693 no. surface atoms = 1141 nbur = 1290 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 279 mr = 2953 m= 1 mr = 13 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 0.3600000 number of dielectric boundary points 3330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2468 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7465 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2674973E-09 -1.6923055E-09 midg,1,midg; midg,igrid,midg 6.5399564E-10 4.8204494E-09 1,midg,midg; igrid,midg,midg 3.9420014E-10 6.8342882E-09 gauss-seidel spectral radius is 0.9854484 estimated iterations to convergence 68 setup time was (sec) 0.6600000 now iterating at: 15:10:45 rms-change max change #iterations 0.1024761 17.43250 at 10iterations 8.5812490E-03 1.422388 at 20iterations 7.5426826E-04 0.1177669 at 30iterations 7.6122531E-05 1.1220932E-02 at 40iterations 1.1316270E-05 1.6231537E-03 at 50iterations finished qdiffx linear iterations at : 15:10:49 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 1.1316270E-05 1.6231537E-03 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 15:10:50 4.406u 0.402s 0:05.15 93.2% 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 15:10:50 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2431 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.789185 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): 13.10300 72.79500 ymin,ymax (A): -13.31000 32.73600 zmin,zma (A): -3.179000 51.67100 x,y,z range (A): 59.69200 46.04600 54.85000 scale (grids/A): 1.789185 object centre (A): 42.94900 9.712999 24.24600 number of atom coordinates read : 2431 total number of charged atoms : 2355 net assigned charge : 8.500020 assigned positive charge : 369.5671 centred at (gu) : 91.60330 87.25433 91.11277 assigned negative charge : -361.0677 centred at (gu) : 91.32520 86.98965 91.58028 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 64974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24693 grid for indexing accessible points = 1.400000 m= 21005 mr = 42518 m= 2669 mr = 14133 m= 102 mr = 1344 m= 0 mr = 12 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 30743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 18347 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) : 0.5963948 object centre at (A) : 42.94900 9.712999 24.24600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0022409E-02 -5.3374604E-03 midg,1,midg; midg,igrid,midg 1.0417943E-02 9.3348268E-03 1,midg,midg; igrid,midg,midg 2.7523519E-02 4.9946781E-02 gauss-seidel spectral radius is 0.9984512 estimated iterations to convergence 202 setup time was (sec) 0.9700000 now iterating at: 15:10:51 rms-change max change #iterations 3.567966 192.2637 at 10iterations 1.587904 56.85294 at 20iterations 0.7040226 26.42672 at 30iterations 0.3114757 10.55768 at 40iterations 0.1382992 5.548836 at 50iterations 6.1658539E-02 2.130363 at 60iterations 2.7288206E-02 1.003048 at 70iterations 1.2233583E-02 0.3997955 at 80iterations 5.4371534E-03 0.1939105 at 90iterations 2.4243421E-03 9.1033936E-02 at 100iterations 1.0877840E-03 4.2425632E-02 at 110iterations 4.8518294E-04 1.7831802E-02 at 120iterations finished qdiffx linear iterations at : 15:11:00 total time elapsed so far: 9.860000 # loops : 120 mean,max change (kT/e) : 4.8518294E-04 1.7831802E-02 energy calculations done at 9.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.08000 DelPhi exited at 15:11:00 10.088u 0.469s 0:10.88 96.8% 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 Sat Oct 8 2011 at 15:11:01 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2431 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.683777 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): 13.10300 72.79500 ymin,ymax (A): -13.31000 32.73600 zmin,zma (A): -3.179000 51.67100 x,y,z range (A): 59.69200 46.04600 54.85000 scale (grids/A): 2.683777 object centre (A): 42.94900 9.712999 24.24600 number of atom coordinates read : 2431 total number of charged atoms : 2355 net assigned charge : 8.500020 assigned positive charge : 369.5671 centred at (gu) : 92.40474 85.88140 91.66896 assigned negative charge : -361.0677 centred at (gu) : 91.98768 85.48449 92.37033 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 150266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24693 grid for indexing accessible points = 1.400000 m= 70282 mr = 104063 m= 22322 mr = 54470 m= 4396 mr = 16557 m= 416 mr = 2943 m= 11 mr = 188 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.690000 number of dielectric boundary points 69473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 18834 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) : 1.789185 object centre at (A) : 42.94900 9.712999 24.24600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4317223E-02 -2.3510566E-02 midg,1,midg; midg,igrid,midg 0.1352717 7.9495408E-02 1,midg,midg; igrid,midg,midg 0.5272583 1.014499 gauss-seidel spectral radius is 0.9992224 estimated iterations to convergence 283 setup time was (sec) 2.070000 now iterating at: 15:11:03 rms-change max change #iterations 8.951017 273.2198 at 10iterations 5.265432 144.4003 at 20iterations 3.060779 81.70200 at 30iterations 1.766831 41.39083 at 40iterations 1.013574 22.55278 at 50iterations 0.5812593 11.51715 at 60iterations 0.3325841 8.143875 at 70iterations 0.1889913 3.716726 at 80iterations 0.1075852 2.145931 at 90iterations 6.1315652E-02 1.464673 at 100iterations 3.4833111E-02 0.7020116 at 110iterations 1.9794386E-02 0.4188080 at 120iterations 1.1202669E-02 0.2361495 at 130iterations 6.3673086E-03 0.1307087 at 140iterations 3.6145148E-03 7.7415466E-02 at 150iterations 2.0469711E-03 4.2113304E-02 at 160iterations 1.1618771E-03 2.3159981E-02 at 170iterations 6.5978942E-04 1.4471054E-02 at 180iterations finished qdiffx linear iterations at : 15:11:19 total time elapsed so far: 17.80000 # loops : 180 mean,max change (kT/e) : 6.5978942E-04 1.4471054E-02 energy calculations done at 17.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.04000 DelPhi exited at 15:11:19 18.042u 0.468s 0:18.79 98.4% 0+0k 0+0io 0pf+0w