Sat Oct 15 11:20:17 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+sph2.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 = amb2.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 15 2011 at 11:20:17 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4461 !!! WARNING: HIT 443 has a net charge of 0.5140 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: 0.5041565 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): -2.694000 67.91900 ymin,ymax (A): -11.61900 39.14800 zmin,zma (A): -19.51300 46.06600 x,y,z range (A): 70.61300 50.76700 65.57899 scale (grids/A): 0.5041565 object centre (A): 32.61250 13.76450 13.27650 number of atom coordinates read : 4461 total number of charged atoms : 4306 net assigned charge : -5.485954 assigned positive charge : 676.1850 centred at (gu) : 88.07108 89.81039 90.50121 assigned negative charge : -681.6732 centred at (gu) : 88.15187 89.93349 90.55252 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7012 nv = 96 ne = 84 npr = 93874 no. pairs analyzed = 93874 no. exposed pairs = 4943 no. arc points = 33500 no. surface atoms = 1688 nbur = 2773 mkacc time = 0.2000000 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 = 1.680000 m= 241 mr = 3942 m= 0 mr = 13 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.4100000 number of dielectric boundary points 3298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3379 ## 514 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9515 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9527401E-11 -1.7981297E-10 midg,1,midg; midg,igrid,midg 1.7370699E-10 -2.7972830E-10 1,midg,midg; igrid,midg,midg 1.5170443E-10 -1.2798702E-10 gauss-seidel spectral radius is 0.9798474 estimated iterations to convergence 58 setup time was (sec) 0.6400000 now iterating at: 11:20:17 rms-change max change #iterations 6.0833216E-02 10.83231 at 10iterations 3.6366058E-03 0.5562544 at 20iterations 4.0853268E-04 6.2469482E-02 at 30iterations 8.7915236E-05 1.1728764E-02 at 40iterations 2.1357802E-05 2.9716492E-03 at 50iterations finished qdiffx linear iterations at : 11:20:20 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 2.1357802E-05 2.9716492E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 11:20:20 3.282u 0.139s 0:03.81 89.5% 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 15 2011 at 11:20:21 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4461 !!! WARNING: HIT 443 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.512469 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): -2.694000 67.91900 ymin,ymax (A): -11.61900 39.14800 zmin,zma (A): -19.51300 46.06600 x,y,z range (A): 70.61300 50.76700 65.57899 scale (grids/A): 1.512469 object centre (A): 32.61250 13.76450 13.27650 number of atom coordinates read : 4461 total number of charged atoms : 4306 net assigned charge : -5.485954 assigned positive charge : 676.1850 centred at (gu) : 84.21197 89.42987 91.50249 assigned negative charge : -681.6732 centred at (gu) : 84.45517 89.80021 91.65748 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 80000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33500 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23588 mr = 57650 m= 2023 mr = 16439 m= 26 mr = 934 m= 0 mr = 1 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2391 time to turn everything in is 0.5600000 number of dielectric boundary points 30613 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 475 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 32242 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) : 0.5041565 object centre at (A) : 32.61250 13.76450 13.27650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9627953E-03 -1.8292071E-02 midg,1,midg; midg,igrid,midg 2.2187706E-03 -9.8655280E-03 1,midg,midg; igrid,midg,midg 1.4311658E-02 -8.5834796E-03 gauss-seidel spectral radius is 0.9980024 estimated iterations to convergence 178 setup time was (sec) 0.8400000 now iterating at: 11:20:22 rms-change max change #iterations 3.561396 153.8186 at 10iterations 1.423738 50.74108 at 20iterations 0.5696725 21.60411 at 30iterations 0.2282652 7.480625 at 40iterations 9.1340072E-02 3.473662 at 50iterations 3.6761168E-02 1.238334 at 60iterations 1.4843831E-02 0.5851784 at 70iterations 6.0109920E-03 0.2039324 at 80iterations 2.4979345E-03 9.2338562E-02 at 90iterations 1.0703285E-03 3.5511017E-02 at 100iterations 4.9153937E-04 1.7755508E-02 at 110iterations 2.4565530E-04 7.9612732E-03 at 120iterations finished qdiffx linear iterations at : 11:20:28 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 2.4565530E-04 7.9612732E-03 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 11:20:28 7.000u 0.174s 0:07.68 93.3% 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 15 2011 at 11:20:28 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4461 !!! WARNING: HIT 443 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.268704 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): -2.694000 67.91900 ymin,ymax (A): -11.61900 39.14800 zmin,zma (A): -19.51300 46.06600 x,y,z range (A): 70.61300 50.76700 65.57899 scale (grids/A): 2.268704 object centre (A): 32.61250 13.76450 13.27650 number of atom coordinates read : 4461 total number of charged atoms : 4306 net assigned charge : -5.485954 assigned positive charge : 676.1850 centred at (gu) : 81.31767 89.14477 92.25363 assigned negative charge : -681.6732 centred at (gu) : 81.68260 89.70013 92.48614 start vw surface at 0.1900000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 186869 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33500 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 85143 mr = 140849 m= 21827 mr = 68663 m= 2926 mr = 16402 m= 118 mr = 1811 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 7979 time to turn everything in is 1.300000 number of dielectric boundary points 69132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 34349 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) : 1.512469 object centre at (A) : 32.61250 13.76450 13.27650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1927874 -0.3822005 midg,1,midg; midg,igrid,midg 2.7843302E-02 -0.1590409 1,midg,midg; igrid,midg,midg 0.3276304 -0.5341392 gauss-seidel spectral radius is 0.9991058 estimated iterations to convergence 264 setup time was (sec) 1.600000 now iterating at: 11:20:30 rms-change max change #iterations 9.615303 344.5387 at 10iterations 5.367810 119.6713 at 20iterations 2.974293 74.14685 at 30iterations 1.641262 35.17874 at 40iterations 0.9034808 21.89951 at 50iterations 0.4956393 10.98305 at 60iterations 0.2707549 5.482719 at 70iterations 0.1481818 2.895396 at 80iterations 8.0787987E-02 1.616780 at 90iterations 4.4146407E-02 0.8177643 at 100iterations 2.4119105E-02 0.4465332 at 110iterations 1.3159389E-02 0.2584579 at 120iterations 7.1752337E-03 0.1506557 at 130iterations 3.9288290E-03 8.0322981E-02 at 140iterations 2.1576940E-03 4.2934418E-02 at 150iterations 1.1913577E-03 2.1846771E-02 at 160iterations 6.6799548E-04 1.5035152E-02 at 170iterations 3.8028564E-04 7.4203163E-03 at 180iterations finished qdiffx linear iterations at : 11:20:40 total time elapsed so far: 11.17000 # loops : 180 mean,max change (kT/e) : 3.8028564E-04 7.4203163E-03 energy calculations done at 11.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.34000 DelPhi exited at 11:20:40 11.343u 0.172s 0:11.99 95.9% 0+0k 0+0io 0pf+0w