Mon Oct 10 14:01:16 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 14:01:16 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 = 2420 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: 0.6876968 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): -14.05400 37.71300 ymin,ymax (A): 0.6020001 44.45100 zmin,zma (A): -7.365000 44.09000 x,y,z range (A): 51.76700 43.84900 51.45500 scale (grids/A): 0.6876968 object centre (A): 11.82950 22.52650 18.36250 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 370.2410 centred at (gu) : 90.87422 91.20518 90.07516 assigned negative charge : -366.7416 centred at (gu) : 91.06857 91.26404 90.04281 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7622 nv = 96 ne = 84 npr = 48787 no. pairs analyzed = 48787 no. exposed pairs = 3048 no. arc points = 21122 no. surface atoms = 1017 nbur = 1403 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4209 m= 0 mr = 71 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1966 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8746 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2548434E-09 3.1663568E-08 midg,1,midg; midg,igrid,midg 3.2198265E-08 -3.5587928E-09 1,midg,midg; igrid,midg,midg 7.5097077E-08 -6.4608599E-08 gauss-seidel spectral radius is 0.9890167 estimated iterations to convergence 78 setup time was (sec) 0.3800000 now iterating at: 14:01:17 rms-change max change #iterations 0.1944326 26.38666 at 10iterations 2.2817748E-02 3.018318 at 20iterations 3.0486118E-03 0.4046135 at 30iterations 6.3226267E-04 9.4924927E-02 at 40iterations 2.0323289E-04 3.2630920E-02 at 50iterations finished qdiffx linear iterations at : 14:01:20 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.0323289E-04 3.2630920E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 14:01:20 3.325u 0.163s 0:03.89 89.4% 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 14:01:20 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 = 2420 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: 2.063091 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): -14.05400 37.71300 ymin,ymax (A): 0.6020001 44.45100 zmin,zma (A): -7.365000 44.09000 x,y,z range (A): 51.76700 43.84900 51.45500 scale (grids/A): 2.063091 object centre (A): 11.82950 22.52650 18.36250 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 370.2410 centred at (gu) : 92.62226 93.61497 90.22515 assigned negative charge : -366.7416 centred at (gu) : 93.20557 93.79190 90.12817 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21122 grid for indexing accessible points = 1.400000 m= 30920 mr = 55614 m= 5774 mr = 23034 m= 557 mr = 3789 m= 9 mr = 309 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 34875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 18072 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) : 0.6876968 object centre at (A) : 11.82950 22.52650 18.36250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4501486E-02 2.1823812E-02 midg,1,midg; midg,igrid,midg 3.4133598E-02 3.4937225E-03 1,midg,midg; igrid,midg,midg 2.0982817E-02 -6.3504107E-02 gauss-seidel spectral radius is 0.9988096 estimated iterations to convergence 229 setup time was (sec) 0.6200000 now iterating at: 14:01:21 rms-change max change #iterations 4.851589 198.6910 at 10iterations 2.381009 73.17220 at 20iterations 1.173704 34.68544 at 30iterations 0.5787781 18.57339 at 40iterations 0.2857732 8.131739 at 50iterations 0.1410114 4.258035 at 60iterations 6.9404639E-02 1.908075 at 70iterations 3.4375399E-02 1.093655 at 80iterations 1.7020587E-02 0.5317183 at 90iterations 8.4746815E-03 0.2447338 at 100iterations 4.2922804E-03 0.1265469 at 110iterations 2.2227105E-03 7.1830750E-02 at 120iterations finished qdiffx linear iterations at : 14:01:28 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 2.2227105E-03 7.1830750E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 14:01:29 7.719u 0.189s 0:09.01 87.5% 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 14:01:29 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 = 2420 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: 3.094636 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): -14.05400 37.71300 ymin,ymax (A): 0.6020001 44.45100 zmin,zma (A): -7.365000 44.09000 x,y,z range (A): 51.76700 43.84900 51.45500 scale (grids/A): 3.094636 object centre (A): 11.82950 22.52650 18.36250 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 370.2410 centred at (gu) : 93.93315 95.42231 90.33762 assigned negative charge : -366.7416 centred at (gu) : 94.80821 95.68782 90.19220 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 185344 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21122 grid for indexing accessible points = 1.400000 m= 96989 mr = 134382 m= 38477 mr = 79493 m= 10775 mr = 31273 m= 2155 mr = 8280 m= 280 mr = 1680 m= 4 mr = 183 m= 0 mr = 0 time to grow re-entrant surface = 0.6100001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 78733 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 18224 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) : 2.063091 object centre at (A) : 11.82950 22.52650 18.36250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3684519 9.8794125E-02 midg,1,midg; midg,igrid,midg 0.3083166 -6.5220669E-02 1,midg,midg; igrid,midg,midg 0.3531660 -0.6700377 gauss-seidel spectral radius is 0.9992957 estimated iterations to convergence 297 setup time was (sec) 1.460000 now iterating at: 14:01:31 rms-change max change #iterations 10.93433 458.1814 at 10iterations 6.482433 157.5498 at 20iterations 3.838061 79.62881 at 30iterations 2.259554 44.05342 at 40iterations 1.329396 29.99136 at 50iterations 0.7831604 18.00371 at 60iterations 0.4577836 8.676226 at 70iterations 0.2682524 4.508400 at 80iterations 0.1570524 3.034405 at 90iterations 9.2080735E-02 1.519169 at 100iterations 5.4000970E-02 0.9242706 at 110iterations 3.1759966E-02 0.5295219 at 120iterations 1.8826792E-02 0.3219299 at 130iterations 1.1242080E-02 0.1901550 at 140iterations 6.8774954E-03 0.1259136 at 150iterations 4.3741493E-03 8.7982178E-02 at 160iterations 2.9257559E-03 6.2103271E-02 at 170iterations 2.0892208E-03 4.5688629E-02 at 180iterations finished qdiffx linear iterations at : 14:01:42 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 2.0892208E-03 4.5688629E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 14:01:43 12.752u 0.198s 0:13.46 96.1% 0+0k 0+0io 0pf+0w