Tue Oct 11 04:22:18 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 Tue Oct 11 2011 at 04:22:18 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 = 2689 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6495520 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): -11.24300 36.67800 ymin,ymax (A): -25.46400 22.54900 zmin,zma (A): -9.972000 44.83500 x,y,z range (A): 47.92100 48.01300 54.80700 scale (grids/A): 0.6495520 object centre (A): 12.71750 -1.457500 17.43150 number of atom coordinates read : 2689 total number of charged atoms : 2540 net assigned charge : -0.4999839 assigned positive charge : 407.7058 centred at (gu) : 90.01553 90.22715 91.98611 assigned negative charge : -408.2064 centred at (gu) : 89.75908 90.04596 91.93322 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7457 nv = 96 ne = 84 npr = 55997 no. pairs analyzed = 55997 no. exposed pairs = 3174 no. arc points = 21832 no. surface atoms = 1072 nbur = 1617 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 4340 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3000000 number of dielectric boundary points 3513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2191 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9107 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2574639E-09 1.1103662E-08 midg,1,midg; midg,igrid,midg -2.8866316E-08 2.8292376E-08 1,midg,midg; igrid,midg,midg -4.2628535E-08 3.8406295E-08 gauss-seidel spectral radius is 0.9877197 estimated iterations to convergence 74 setup time was (sec) 0.5100000 now iterating at: 04:22:19 rms-change max change #iterations 0.1604120 24.96579 at 10iterations 1.6741019E-02 2.114636 at 20iterations 2.0071599E-03 0.2555046 at 30iterations 3.2429289E-04 5.3085327E-02 at 40iterations 8.0988320E-05 1.1634827E-02 at 50iterations finished qdiffx linear iterations at : 04:22:21 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 8.0988320E-05 1.1634827E-02 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 04:22:22 3.098u 0.152s 0:03.81 85.0% 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 Tue Oct 11 2011 at 04:22:22 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 = 2689 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: 1.948656 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): -11.24300 36.67800 ymin,ymax (A): -25.46400 22.54900 zmin,zma (A): -9.972000 44.83500 x,y,z range (A): 47.92100 48.01300 54.80700 scale (grids/A): 1.948656 object centre (A): 12.71750 -1.457500 17.43150 number of atom coordinates read : 2689 total number of charged atoms : 2540 net assigned charge : -0.4999839 assigned positive charge : 407.7058 centred at (gu) : 90.04624 90.68077 95.95752 assigned negative charge : -408.2064 centred at (gu) : 89.27703 90.13776 95.79961 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80954 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21832 grid for indexing accessible points = 1.400000 m= 30668 mr = 57780 m= 4937 mr = 23263 m= 296 mr = 3235 m= 3 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2425 time to turn everything in is 0.5600000 number of dielectric boundary points 32463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20005 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) : 0.6495520 object centre at (A) : 12.71750 -1.457500 17.43150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5229152E-02 -3.6984633E-03 midg,1,midg; midg,igrid,midg -3.4072850E-02 2.8312802E-02 1,midg,midg; igrid,midg,midg -2.5975417E-02 4.5504145E-02 gauss-seidel spectral radius is 0.9986979 estimated iterations to convergence 220 setup time was (sec) 0.8200000 now iterating at: 04:22:23 rms-change max change #iterations 4.554507 182.1319 at 10iterations 2.180570 66.00537 at 20iterations 1.041588 32.13579 at 30iterations 0.4979925 15.38293 at 40iterations 0.2394804 8.254429 at 50iterations 0.1140866 3.412411 at 60iterations 5.4752726E-02 1.677568 at 70iterations 2.6115371E-02 0.8543396 at 80iterations 1.2632133E-02 0.4039383 at 90iterations 6.1214878E-03 0.1740913 at 100iterations 2.9969630E-03 9.3376160E-02 at 110iterations 1.5216393E-03 4.8294067E-02 at 120iterations finished qdiffx linear iterations at : 04:22:29 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 1.5216393E-03 4.8294067E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 04:22:30 6.955u 0.178s 0:07.66 92.9% 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 Tue Oct 11 2011 at 04:22:30 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 = 2689 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.922984 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): -11.24300 36.67800 ymin,ymax (A): -25.46400 22.54900 zmin,zma (A): -9.972000 44.83500 x,y,z range (A): 47.92100 48.01300 54.80700 scale (grids/A): 2.922984 object centre (A): 12.71750 -1.457500 17.43150 number of atom coordinates read : 2689 total number of charged atoms : 2540 net assigned charge : -0.4999839 assigned positive charge : 407.7058 centred at (gu) : 90.06924 91.02103 98.93619 assigned negative charge : -408.2064 centred at (gu) : 88.91548 90.20648 98.69923 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 187244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21832 grid for indexing accessible points = 1.400000 m= 98554 mr = 139327 m= 36651 mr = 82155 m= 9047 mr = 30207 m= 1391 mr = 7007 m= 98 mr = 987 m= 0 mr = 45 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 8078 time to turn everything in is 1.420000 number of dielectric boundary points 73257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 20319 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) : 1.948656 object centre at (A) : 12.71750 -1.457500 17.43150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4132404 8.5715614E-02 midg,1,midg; midg,igrid,midg -0.3946249 0.3494117 1,midg,midg; igrid,midg,midg -0.1892649 0.3679400 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.700000 now iterating at: 04:22:32 rms-change max change #iterations 10.52486 497.6406 at 10iterations 6.164021 145.1823 at 20iterations 3.594682 74.84800 at 30iterations 2.094801 39.99251 at 40iterations 1.218200 23.72049 at 50iterations 0.7067389 13.23841 at 60iterations 0.4109569 7.425356 at 70iterations 0.2378414 4.059277 at 80iterations 0.1378819 2.534058 at 90iterations 7.9826832E-02 1.390119 at 100iterations 4.6381198E-02 0.8018875 at 110iterations 2.7002057E-02 0.4822974 at 120iterations 1.5816541E-02 0.3016548 at 130iterations 9.3754996E-03 0.1667976 at 140iterations 5.6657549E-03 0.1016769 at 150iterations 3.5434156E-03 7.3406219E-02 at 160iterations 2.3232587E-03 4.8221588E-02 at 170iterations 1.6191832E-03 3.4420013E-02 at 180iterations finished qdiffx linear iterations at : 04:22:41 total time elapsed so far: 11.32000 # loops : 180 mean,max change (kT/e) : 1.6191832E-03 3.4420013E-02 energy calculations done at 11.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.49000 DelPhi exited at 04:22:42 11.497u 0.163s 0:12.15 95.8% 0+0k 0+0io 0pf+0w