Sat Oct 8 11:34:40 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 11:34:40 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 = 3177 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: 0.5655552 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): -14.35300 48.59400 ymin,ymax (A): -38.30300 23.26600 zmin,zma (A): -51.45200 11.11600 x,y,z range (A): 62.94700 61.56900 62.56800 scale (grids/A): 0.5655552 object centre (A): 17.12050 -7.518500 -20.16800 number of atom coordinates read : 3177 total number of charged atoms : 3019 net assigned charge : -3.999987 assigned positive charge : 473.2024 centred at (gu) : 88.40733 91.69488 89.52157 assigned negative charge : -477.2040 centred at (gu) : 88.36240 91.69327 89.56268 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6860 nv = 96 ne = 84 npr = 60824 no. pairs analyzed = 60824 no. exposed pairs = 4462 no. arc points = 32700 no. surface atoms = 1500 nbur = 1677 mkacc time = 0.1600000 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 = 1.512000 m= 295 mr = 3192 m= 0 mr = 8 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3272 ## 401 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8683 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9609375E-11 -9.8552455E-10 midg,1,midg; midg,igrid,midg -3.6144371E-10 -7.2470219E-10 1,midg,midg; igrid,midg,midg -1.7022938E-09 8.2645522E-11 gauss-seidel spectral radius is 0.9839044 estimated iterations to convergence 65 setup time was (sec) 0.5900000 now iterating at: 11:34:41 rms-change max change #iterations 8.9212537E-02 13.17352 at 10iterations 6.6607590E-03 1.135283 at 20iterations 4.8902084E-04 8.2681656E-02 at 30iterations 4.9137212E-05 9.2945099E-03 at 40iterations 8.4192998E-06 1.7223358E-03 at 50iterations finished qdiffx linear iterations at : 11:34:45 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 8.4192998E-06 1.7223358E-03 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 11:34:45 4.483u 0.447s 0:05.42 90.7% 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 Sat Oct 8 2011 at 11:34:45 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 = 3177 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: 1.696665 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): -14.35300 48.59400 ymin,ymax (A): -38.30300 23.26600 zmin,zma (A): -51.45200 11.11600 x,y,z range (A): 62.94700 61.56900 62.56800 scale (grids/A): 1.696665 object centre (A): 17.12050 -7.518500 -20.16800 number of atom coordinates read : 3177 total number of charged atoms : 3019 net assigned charge : -3.999987 assigned positive charge : 473.2024 centred at (gu) : 85.22095 95.08354 88.56397 assigned negative charge : -477.2040 centred at (gu) : 85.08716 95.07925 88.68764 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74796 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32700 grid for indexing accessible points = 1.400000 m= 21975 mr = 47261 m= 2159 mr = 14187 m= 60 mr = 914 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 514 time to turn everything in is 0.6100000 number of dielectric boundary points 36628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 375 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 23305 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) : 0.5655552 object centre at (A) : 17.12050 -7.518500 -20.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9535940E-02 2.2444702E-03 midg,1,midg; midg,igrid,midg -6.4706234E-03 2.4726740E-03 1,midg,midg; igrid,midg,midg -1.3760302E-02 8.9129051E-03 gauss-seidel spectral radius is 0.9983643 estimated iterations to convergence 196 setup time was (sec) 0.9400000 now iterating at: 11:34:47 rms-change max change #iterations 3.754357 165.6668 at 10iterations 1.626162 64.08179 at 20iterations 0.7057753 24.99944 at 30iterations 0.3071116 10.12249 at 40iterations 0.1333079 4.491352 at 50iterations 5.7939500E-02 2.112798 at 60iterations 2.5266480E-02 0.7999020 at 70iterations 1.0986964E-02 0.4109842 at 80iterations 4.7830991E-03 0.1615984 at 90iterations 2.0740507E-03 7.1853638E-02 at 100iterations 9.0575975E-04 3.2520294E-02 at 110iterations 3.9491890E-04 1.4411926E-02 at 120iterations finished qdiffx linear iterations at : 11:34:56 total time elapsed so far: 10.62000 # loops : 120 mean,max change (kT/e) : 3.9491890E-04 1.4411926E-02 energy calculations done at 10.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.79000 DelPhi exited at 11:34:57 10.792u 0.482s 0:11.60 97.1% 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 11:34:57 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 = 3177 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: 2.544998 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): -14.35300 48.59400 ymin,ymax (A): -38.30300 23.26600 zmin,zma (A): -51.45200 11.11600 x,y,z range (A): 62.94700 61.56900 62.56800 scale (grids/A): 2.544998 object centre (A): 17.12050 -7.518500 -20.16800 number of atom coordinates read : 3177 total number of charged atoms : 3019 net assigned charge : -3.999987 assigned positive charge : 473.2024 centred at (gu) : 82.83130 97.62518 87.84565 assigned negative charge : -477.2040 centred at (gu) : 82.63052 97.61892 88.03128 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 173386 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32700 grid for indexing accessible points = 1.400000 m= 75649 mr = 116545 m= 21342 mr = 57482 m= 3240 mr = 15219 m= 202 mr = 1905 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 1699 time to turn everything in is 1.510000 number of dielectric boundary points 82612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 24133 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) : 1.696665 object centre at (A) : 17.12050 -7.518500 -20.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5207773 0.3874454 midg,1,midg; midg,igrid,midg -0.1046094 3.8218651E-02 1,midg,midg; igrid,midg,midg -0.1569677 9.1083936E-02 gauss-seidel spectral radius is 0.9992174 estimated iterations to convergence 282 setup time was (sec) 1.880000 now iterating at: 11:34:59 rms-change max change #iterations 9.722341 376.3008 at 10iterations 5.703700 142.9286 at 20iterations 3.297352 80.05360 at 30iterations 1.902641 43.88246 at 40iterations 1.092742 25.08521 at 50iterations 0.6262764 13.64504 at 60iterations 0.3568850 8.264322 at 70iterations 0.2032824 4.608115 at 80iterations 0.1155808 2.359261 at 90iterations 6.5632828E-02 1.459327 at 100iterations 3.7227876E-02 0.7883377 at 110iterations 2.1056233E-02 0.4391761 at 120iterations 1.1958761E-02 0.2322235 at 130iterations 6.7551588E-03 0.1251092 at 140iterations 3.8248787E-03 7.5250626E-02 at 150iterations 2.1647979E-03 4.0496826E-02 at 160iterations 1.2236970E-03 2.9594421E-02 at 170iterations 6.9539325E-04 1.4787674E-02 at 180iterations finished qdiffx linear iterations at : 11:35:15 total time elapsed so far: 17.97000 # loops : 180 mean,max change (kT/e) : 6.9539325E-04 1.4787674E-02 energy calculations done at 17.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.14000 DelPhi exited at 11:35:16 18.146u 0.491s 0:18.92 98.4% 0+0k 0+0io 0pf+0w