Sat Oct 8 20:15:08 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+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 20:15:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 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: 0.6169630 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): -31.26600 17.40000 ymin,ymax (A): -23.45400 22.66600 zmin,zma (A): -12.64000 45.06200 x,y,z range (A): 48.66600 46.12000 57.70200 scale (grids/A): 0.6169630 object centre (A): -6.933001 -0.3940001 16.21100 number of atom coordinates read : 2605 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 88.54150 89.22930 89.61359 assigned negative charge : -387.9955 centred at (gu) : 88.43291 89.27519 89.50127 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6389 nv = 96 ne = 84 npr = 54691 no. pairs analyzed = 54691 no. exposed pairs = 2999 no. arc points = 21623 no. surface atoms = 1015 nbur = 1590 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 278 mr = 3518 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 0.2000000 number of dielectric boundary points 3110 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2207 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8022 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2155417E-09 8.9697831E-09 midg,1,midg; midg,igrid,midg 6.8928934E-09 2.3326788E-10 1,midg,midg; igrid,midg,midg -5.1153086E-09 6.9304402E-09 gauss-seidel spectral radius is 0.9863908 estimated iterations to convergence 70 setup time was (sec) 0.3700000 now iterating at: 20:15:09 rms-change max change #iterations 0.1218046 20.17471 at 10iterations 1.1082804E-02 1.698734 at 20iterations 9.9017029E-04 0.1506720 at 30iterations 9.5056268E-05 1.4549255E-02 at 40iterations 8.7245598E-06 1.2969971E-03 at 50iterations finished qdiffx linear iterations at : 20:15:11 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 8.7245598E-06 1.2969971E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 20:15:12 3.336u 0.172s 0:03.78 92.5% 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 Sat Oct 8 2011 at 20:15:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 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: 1.850889 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): -31.26600 17.40000 ymin,ymax (A): -23.45400 22.66600 zmin,zma (A): -12.64000 45.06200 x,y,z range (A): 48.66600 46.12000 57.70200 scale (grids/A): 1.850889 object centre (A): -6.933001 -0.3940001 16.21100 number of atom coordinates read : 2605 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 85.62423 87.68733 88.84038 assigned negative charge : -387.9955 centred at (gu) : 85.29841 87.82526 88.50357 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21623 grid for indexing accessible points = 1.400000 m= 23596 mr = 48514 m= 3281 mr = 17370 m= 145 mr = 2003 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 3986 time to turn everything in is 0.3400000 number of dielectric boundary points 28691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19345 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) : 0.6169630 object centre at (A) : -6.933001 -0.3940001 16.21100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8330479E-02 2.8299130E-02 midg,1,midg; midg,igrid,midg 1.0884575E-02 1.2199555E-03 1,midg,midg; igrid,midg,midg -3.8666360E-03 3.1703360E-02 gauss-seidel spectral radius is 0.9985513 estimated iterations to convergence 208 setup time was (sec) 0.5700000 now iterating at: 20:15:13 rms-change max change #iterations 3.956289 153.3131 at 10iterations 1.814053 63.09554 at 20iterations 0.8284805 27.23370 at 30iterations 0.3802732 11.62084 at 40iterations 0.1741032 5.997639 at 50iterations 7.9920195E-02 2.528839 at 60iterations 3.6537208E-02 1.186197 at 70iterations 1.6728414E-02 0.5572057 at 80iterations 7.6570679E-03 0.2701511 at 90iterations 3.5212226E-03 0.1191902 at 100iterations 1.6073702E-03 5.5166245E-02 at 110iterations 7.3723198E-04 2.4680138E-02 at 120iterations finished qdiffx linear iterations at : 20:15:20 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 7.3723198E-04 2.4680138E-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) 7.730000 DelPhi exited at 20:15:20 7.736u 0.188s 0:08.30 95.3% 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 20:15:20 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 = 2605 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: 2.776334 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): -31.26600 17.40000 ymin,ymax (A): -23.45400 22.66600 zmin,zma (A): -12.64000 45.06200 x,y,z range (A): 48.66600 46.12000 57.70200 scale (grids/A): 2.776334 object centre (A): -6.933001 -0.3940001 16.21100 number of atom coordinates read : 2605 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 83.43621 86.53096 88.26049 assigned negative charge : -387.9955 centred at (gu) : 82.94761 86.73792 87.75534 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 161379 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21623 grid for indexing accessible points = 1.400000 m= 78391 mr = 117818 m= 26234 mr = 64329 m= 5617 mr = 20966 m= 683 mr = 4124 m= 33 mr = 441 m= 0 mr = 9 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 13325 time to turn everything in is 0.8500000 number of dielectric boundary points 64650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 19720 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) : 1.850889 object centre at (A) : -6.933001 -0.3940001 16.21100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1372447 0.3698740 midg,1,midg; midg,igrid,midg 0.1256928 -6.3703326E-03 1,midg,midg; igrid,midg,midg -3.8989183E-02 0.4360417 gauss-seidel spectral radius is 0.9992277 estimated iterations to convergence 284 setup time was (sec) 1.080000 now iterating at: 20:15:21 rms-change max change #iterations 9.409530 346.6651 at 10iterations 5.396437 127.6175 at 20iterations 3.079289 81.56341 at 30iterations 1.754651 38.35682 at 40iterations 0.9973141 19.78336 at 50iterations 0.5674852 11.09560 at 60iterations 0.3225856 6.370804 at 70iterations 0.1831262 3.695433 at 80iterations 0.1040720 1.969078 at 90iterations 5.9189130E-02 1.093653 at 100iterations 3.3563554E-02 0.7196655 at 110iterations 1.9081505E-02 0.3539906 at 120iterations 1.0793765E-02 0.2030869 at 130iterations 6.1459248E-03 0.1195214 at 140iterations 3.4847457E-03 6.7882538E-02 at 150iterations 1.9789257E-03 3.6588669E-02 at 160iterations 1.1235429E-03 2.0712376E-02 at 170iterations 6.3909986E-04 1.1518478E-02 at 180iterations finished qdiffx linear iterations at : 20:15:32 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 6.3909986E-04 1.1518478E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 20:15:33 12.216u 0.195s 0:12.73 97.4% 0+0k 0+0io 0pf+0w