Mon Oct 10 09:44:20 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 09:44:20 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 = 2715 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5944628 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): -17.46600 31.83400 ymin,ymax (A): -60.43200 -0.8370000 zmin,zma (A): 8.9999437E-03 59.89500 x,y,z range (A): 49.30000 59.59500 59.88600 scale (grids/A): 0.5944628 object centre (A): 7.184000 -30.63450 29.95200 number of atom coordinates read : 2715 total number of charged atoms : 2565 net assigned charge : 6.000019 assigned positive charge : 393.1631 centred at (gu) : 88.75244 88.17970 87.43475 assigned negative charge : -387.1635 centred at (gu) : 88.82736 88.05389 87.31652 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6574 nv = 96 ne = 84 npr = 52282 no. pairs analyzed = 52282 no. exposed pairs = 4242 no. arc points = 30920 no. surface atoms = 1403 nbur = 1312 mkacc time = 0.1100000 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 = 1.456000 m= 349 mr = 2835 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2984 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8097 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5925797E-09 3.2464162E-09 midg,1,midg; midg,igrid,midg -2.5006970E-09 3.9786325E-09 1,midg,midg; igrid,midg,midg 6.0002359E-09 1.5729426E-11 gauss-seidel spectral radius is 0.9853896 estimated iterations to convergence 68 setup time was (sec) 0.5400000 now iterating at: 09:44:20 rms-change max change #iterations 0.1039089 17.61716 at 10iterations 8.4714955E-03 1.503799 at 20iterations 7.0407894E-04 0.1013927 at 30iterations 6.1468811E-05 9.4451904E-03 at 40iterations 7.3833680E-06 9.4604492E-04 at 50iterations finished qdiffx linear iterations at : 09:44:23 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 7.3833680E-06 9.4604492E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 09:44:24 3.440u 0.210s 0:04.25 85.8% 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 Mon Oct 10 2011 at 09:44:24 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 = 2715 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.783388 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): -17.46600 31.83400 ymin,ymax (A): -60.43200 -0.8370000 zmin,zma (A): 8.9999437E-03 59.89500 x,y,z range (A): 49.30000 59.59500 59.88600 scale (grids/A): 1.783388 object centre (A): 7.184000 -30.63450 29.95200 number of atom coordinates read : 2715 total number of charged atoms : 2565 net assigned charge : 6.000019 assigned positive charge : 393.1631 centred at (gu) : 86.25692 84.53847 82.30381 assigned negative charge : -387.1635 centred at (gu) : 86.48175 84.16151 81.94934 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69609 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30920 grid for indexing accessible points = 1.400000 m= 22770 mr = 41892 m= 3224 mr = 14510 m= 132 mr = 1489 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 37831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20033 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) : 0.5944628 object centre at (A) : 7.184000 -30.63450 29.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5097645E-04 4.2657414E-03 midg,1,midg; midg,igrid,midg 2.3570715E-02 3.5598531E-02 1,midg,midg; igrid,midg,midg 1.2243994E-02 3.3408394E-03 gauss-seidel spectral radius is 0.9984832 estimated iterations to convergence 204 setup time was (sec) 0.8500000 now iterating at: 09:44:25 rms-change max change #iterations 3.714233 165.7577 at 10iterations 1.658112 53.68344 at 20iterations 0.7444863 29.87202 at 30iterations 0.3323125 11.21194 at 40iterations 0.1492415 5.218102 at 50iterations 6.6889279E-02 2.662830 at 60iterations 2.9925454E-02 1.053015 at 70iterations 1.3430396E-02 0.4945536 at 80iterations 6.0179010E-03 0.2236423 at 90iterations 2.7149387E-03 0.1035969 at 100iterations 1.2160081E-03 4.1853905E-02 at 110iterations 5.4419017E-04 1.8383026E-02 at 120iterations finished qdiffx linear iterations at : 09:44:33 total time elapsed so far: 8.390000 # loops : 120 mean,max change (kT/e) : 5.4419017E-04 1.8383026E-02 energy calculations done at 8.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.570000 DelPhi exited at 09:44:33 8.577u 0.246s 0:09.50 92.7% 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 09:44:33 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 = 2715 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.675083 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): -17.46600 31.83400 ymin,ymax (A): -60.43200 -0.8370000 zmin,zma (A): 8.9999437E-03 59.89500 x,y,z range (A): 49.30000 59.59500 59.88600 scale (grids/A): 2.675083 object centre (A): 7.184000 -30.63450 29.95200 number of atom coordinates read : 2715 total number of charged atoms : 2565 net assigned charge : 6.000019 assigned positive charge : 393.1631 centred at (gu) : 84.38523 81.80765 78.45564 assigned negative charge : -387.1635 centred at (gu) : 84.72254 81.24221 77.92386 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 160693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30920 grid for indexing accessible points = 1.400000 m= 72962 mr = 103494 m= 25105 mr = 53953 m= 5231 mr = 18138 m= 510 mr = 3222 m= 14 mr = 221 m= 0 mr = 2 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 85485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 20511 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) : 1.783388 object centre at (A) : 7.184000 -30.63450 29.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1432629E-02 1.2572573E-02 midg,1,midg; midg,igrid,midg 0.4843805 0.4713309 1,midg,midg; igrid,midg,midg 6.9410555E-02 1.9916447E-02 gauss-seidel spectral radius is 0.9992459 estimated iterations to convergence 287 setup time was (sec) 1.530000 now iterating at: 09:44:35 rms-change max change #iterations 9.428605 271.6731 at 10iterations 5.646019 151.4066 at 20iterations 3.330139 88.14502 at 30iterations 1.946794 45.78960 at 40iterations 1.130694 29.58595 at 50iterations 0.6573754 15.95094 at 60iterations 0.3784618 8.594883 at 70iterations 0.2180925 4.788333 at 80iterations 0.1255185 3.026752 at 90iterations 7.2326638E-02 1.687943 at 100iterations 4.1454986E-02 0.8260095 at 110iterations 2.3737885E-02 0.4800839 at 120iterations 1.3614939E-02 0.3084412 at 130iterations 7.7848788E-03 0.1788397 at 140iterations 4.4585695E-03 8.6365938E-02 at 150iterations 2.5491905E-03 5.2661896E-02 at 160iterations 1.4559275E-03 2.8298378E-02 at 170iterations 8.3479955E-04 1.7852783E-02 at 180iterations finished qdiffx linear iterations at : 09:44:45 total time elapsed so far: 10.98000 # loops : 180 mean,max change (kT/e) : 8.3479955E-04 1.7852783E-02 energy calculations done at 10.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.16000 DelPhi exited at 09:44:45 11.165u 0.172s 0:11.97 94.6% 0+0k 0+0io 0pf+0w