Sun Oct 9 08:17:18 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 Sun Oct 9 2011 at 08:17:18 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 = 5677 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4845845 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): 17.13400 84.09500 ymin,ymax (A): 19.08500 85.74000 zmin,zma (A): -5.173000 68.29200 x,y,z range (A): 66.96100 66.65500 73.46500 scale (grids/A): 0.4845845 object centre (A): 50.61450 52.41250 31.55950 number of atom coordinates read : 5677 total number of charged atoms : 5510 net assigned charge : -6.999978 assigned positive charge : 849.8716 centred at (gu) : 90.14468 89.20206 91.39607 assigned negative charge : -856.8788 centred at (gu) : 90.13171 89.23563 91.45569 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8396 nv = 96 ne = 84 npr = 112834 no. pairs analyzed = 112834 no. exposed pairs = 7455 no. arc points = 51103 no. surface atoms = 2505 nbur = 3172 mkacc time = 0.2400000 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 = 1.764000 m= 280 mr = 4160 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.5100000 number of dielectric boundary points 4516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4776 ## 756 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 11335 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8822907E-11 -1.2760473E-10 midg,1,midg; midg,igrid,midg 4.7370554E-12 -4.9046565E-11 1,midg,midg; igrid,midg,midg -3.9505024E-11 -1.6786740E-11 gauss-seidel spectral radius is 0.9783012 estimated iterations to convergence 56 setup time was (sec) 0.7300000 now iterating at: 08:17:19 rms-change max change #iterations 5.6395855E-02 9.548294 at 10iterations 3.0477813E-03 0.4590530 at 20iterations 3.7410043E-04 9.4306946E-02 at 30iterations 9.7249751E-05 2.5384903E-02 at 40iterations 2.8438604E-05 7.1716309E-03 at 50iterations finished qdiffx linear iterations at : 08:17:21 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 2.8438604E-05 7.1716309E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 08:17:21 3.335u 0.136s 0:03.76 92.0% 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 Sun Oct 9 2011 at 08:17:22 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 = 5677 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.453754 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): 17.13400 84.09500 ymin,ymax (A): 19.08500 85.74000 zmin,zma (A): -5.173000 68.29200 x,y,z range (A): 66.96100 66.65500 73.46500 scale (grids/A): 1.453754 object centre (A): 50.61450 52.41250 31.55950 number of atom coordinates read : 5677 total number of charged atoms : 5510 net assigned charge : -6.999978 assigned positive charge : 849.8716 centred at (gu) : 90.43220 87.60384 94.18655 assigned negative charge : -856.8788 centred at (gu) : 90.39483 87.70679 94.36693 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 95066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51103 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 26468 mr = 63789 m= 1865 mr = 16747 m= 25 mr = 591 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1295 time to turn everything in is 0.6500000 number of dielectric boundary points 42297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 789 ## 16 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 40512 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) : 0.4845845 object centre at (A) : 50.61450 52.41250 31.55950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2604700E-03 -2.5394939E-02 midg,1,midg; midg,igrid,midg -1.1019469E-03 -8.8837510E-03 1,midg,midg; igrid,midg,midg -7.2197430E-04 -3.6953357E-03 gauss-seidel spectral radius is 0.9979734 estimated iterations to convergence 177 setup time was (sec) 0.9100000 now iterating at: 08:17:23 rms-change max change #iterations 3.709392 148.7608 at 10iterations 1.469048 48.54448 at 20iterations 0.5838037 18.17855 at 30iterations 0.2322316 7.541214 at 40iterations 9.2394345E-02 3.208055 at 50iterations 3.6884006E-02 1.124754 at 60iterations 1.4714172E-02 0.5249195 at 70iterations 5.9202523E-03 0.2032795 at 80iterations 2.4139017E-03 7.7512741E-02 at 90iterations 1.0300621E-03 3.7486792E-02 at 100iterations 4.6894542E-04 1.8825531E-02 at 110iterations 2.3985215E-04 1.0364532E-02 at 120iterations finished qdiffx linear iterations at : 08:17:29 total time elapsed so far: 7.020000 # loops : 120 mean,max change (kT/e) : 2.3985215E-04 1.0364532E-02 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.180000 DelPhi exited at 08:17:29 7.179u 0.221s 0:07.69 96.0% 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 Sun Oct 9 2011 at 08:17:29 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 = 5677 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.180630 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): 17.13400 84.09500 ymin,ymax (A): 19.08500 85.74000 zmin,zma (A): -5.173000 68.29200 x,y,z range (A): 66.96100 66.65500 73.46500 scale (grids/A): 2.180630 object centre (A): 50.61450 52.41250 31.55950 number of atom coordinates read : 5677 total number of charged atoms : 5510 net assigned charge : -6.999978 assigned positive charge : 849.8716 centred at (gu) : 90.64796 86.40542 96.27935 assigned negative charge : -856.8788 centred at (gu) : 90.59221 86.56014 96.55035 start vw surface at 0.2200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 221444 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51103 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 96816 mr = 157528 m= 22276 mr = 73429 m= 2431 mr = 15245 m= 66 mr = 1220 m= 0 mr = 6 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 4588 time to turn everything in is 1.570000 number of dielectric boundary points 95605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 43849 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) : 1.453754 object centre at (A) : 50.61450 52.41250 31.55950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1000211 -0.8259462 midg,1,midg; midg,igrid,midg -1.4422370E-02 -0.1785068 1,midg,midg; igrid,midg,midg 7.3546305E-02 -5.2641243E-02 gauss-seidel spectral radius is 0.9991530 estimated iterations to convergence 271 setup time was (sec) 1.870000 now iterating at: 08:17:31 rms-change max change #iterations 10.52483 289.6755 at 10iterations 6.071364 146.7581 at 20iterations 3.466217 77.98680 at 30iterations 1.970808 45.01778 at 40iterations 1.115328 23.58352 at 50iterations 0.6299393 12.47499 at 60iterations 0.3542259 7.610276 at 70iterations 0.1990031 4.532426 at 80iterations 0.1112581 2.207119 at 90iterations 6.2273849E-02 1.244079 at 100iterations 3.4720641E-02 0.6742296 at 110iterations 1.9367155E-02 0.3821411 at 120iterations 1.0820171E-02 0.2255831 at 130iterations 6.0331328E-03 0.1244812 at 140iterations 3.3607041E-03 6.0394287E-02 at 150iterations 1.8811533E-03 3.8406372E-02 at 160iterations 1.0569601E-03 1.9912720E-02 at 170iterations 5.9668475E-04 1.1376381E-02 at 180iterations finished qdiffx linear iterations at : 08:17:41 total time elapsed so far: 11.58000 # loops : 180 mean,max change (kT/e) : 5.9668475E-04 1.1376381E-02 energy calculations done at 11.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.75000 DelPhi exited at 08:17:41 11.749u 0.165s 0:12.22 97.3% 0+0k 0+0io 0pf+0w