Mon Oct 10 16:32:52 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 16:32:52 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 = 2576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6041988 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): 22.74100 69.56500 ymin,ymax (A): -26.34700 32.57400 zmin,zma (A): -6.642000 46.11800 x,y,z range (A): 46.82401 58.92100 52.76000 scale (grids/A): 0.6041988 object centre (A): 46.15300 3.113501 19.73800 number of atom coordinates read : 2576 total number of charged atoms : 2433 net assigned charge : 8.000030 assigned positive charge : 389.5285 centred at (gu) : 88.84786 90.08148 90.42048 assigned negative charge : -381.5294 centred at (gu) : 88.75188 89.98293 90.50259 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6376 nv = 96 ne = 84 npr = 50301 no. pairs analyzed = 50301 no. exposed pairs = 3446 no. arc points = 24856 no. surface atoms = 1150 nbur = 1426 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 3232 m= 3 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2525 ## 279 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7828 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6510411E-09 6.5120798E-10 midg,1,midg; midg,igrid,midg -6.8267642E-11 8.1075813E-09 1,midg,midg; igrid,midg,midg -2.7271373E-11 6.0827539E-09 gauss-seidel spectral radius is 0.9858258 estimated iterations to convergence 69 setup time was (sec) 0.5700000 now iterating at: 16:32:53 rms-change max change #iterations 0.1102977 19.32901 at 10iterations 9.4721075E-03 1.459045 at 20iterations 8.2125590E-04 0.1347427 at 30iterations 7.0861832E-05 1.0395050E-02 at 40iterations 6.2169847E-06 1.0929108E-03 at 50iterations finished qdiffx linear iterations at : 16:32:57 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 6.2169847E-06 1.0929108E-03 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 16:32:57 4.461u 0.382s 0:05.15 93.9% 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 16:32:57 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 = 2576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.812596 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): 22.74100 69.56500 ymin,ymax (A): -26.34700 32.57400 zmin,zma (A): -6.642000 46.11800 x,y,z range (A): 46.82401 58.92100 52.76000 scale (grids/A): 1.812596 object centre (A): 46.15300 3.113501 19.73800 number of atom coordinates read : 2576 total number of charged atoms : 2433 net assigned charge : 8.000030 assigned positive charge : 389.5285 centred at (gu) : 86.54282 90.24378 91.26092 assigned negative charge : -381.5294 centred at (gu) : 86.25541 89.94847 91.50763 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 68347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24856 grid for indexing accessible points = 1.400000 m= 23408 mr = 45227 m= 3049 mr = 16616 m= 153 mr = 1720 m= 0 mr = 43 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 31351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18976 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) : 0.6041988 object centre at (A) : 46.15300 3.113501 19.73800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3733689E-02 1.6773640E-03 midg,1,midg; midg,igrid,midg 2.0563131E-02 3.5061009E-02 1,midg,midg; igrid,midg,midg 2.6680378E-04 2.2811843E-02 gauss-seidel spectral radius is 0.9985021 estimated iterations to convergence 205 setup time was (sec) 0.8500000 now iterating at: 16:32:59 rms-change max change #iterations 3.815363 181.8466 at 10iterations 1.710764 68.36420 at 20iterations 0.7742523 30.44212 at 30iterations 0.3493619 11.49887 at 40iterations 0.1575219 5.546453 at 50iterations 7.1022570E-02 2.186863 at 60iterations 3.2172717E-02 1.089546 at 70iterations 1.4484236E-02 0.5208535 at 80iterations 6.5183421E-03 0.2305987 at 90iterations 2.9555124E-03 0.1079903 at 100iterations 1.3345203E-03 4.8456371E-02 at 110iterations 6.0374808E-04 2.0851135E-02 at 120iterations finished qdiffx linear iterations at : 16:33:09 total time elapsed so far: 10.75000 # loops : 120 mean,max change (kT/e) : 6.0374808E-04 2.0851135E-02 energy calculations done at 10.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.90000 DelPhi exited at 16:33:09 10.909u 0.460s 0:11.89 95.5% 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 Mon Oct 10 2011 at 16:33:09 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 = 2576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.718895 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): 22.74100 69.56500 ymin,ymax (A): -26.34700 32.57400 zmin,zma (A): -6.642000 46.11800 x,y,z range (A): 46.82401 58.92100 52.76000 scale (grids/A): 2.718895 object centre (A): 46.15300 3.113501 19.73800 number of atom coordinates read : 2576 total number of charged atoms : 2433 net assigned charge : 8.000030 assigned positive charge : 389.5285 centred at (gu) : 84.81397 90.36559 91.89104 assigned negative charge : -381.5294 centred at (gu) : 84.38306 89.92268 92.26125 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 158305 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24856 grid for indexing accessible points = 1.400000 m= 76638 mr = 110332 m= 25783 mr = 61288 m= 5068 mr = 19981 m= 644 mr = 3498 m= 25 mr = 442 m= 0 mr = 7 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.440000 number of dielectric boundary points 70915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 19458 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) : 1.812596 object centre at (A) : 46.15300 3.113501 19.73800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1131889 -2.6312200E-02 midg,1,midg; midg,igrid,midg 0.1919781 0.6017765 1,midg,midg; igrid,midg,midg -3.2199025E-02 0.2516004 gauss-seidel spectral radius is 0.9992265 estimated iterations to convergence 284 setup time was (sec) 1.780000 now iterating at: 16:33:12 rms-change max change #iterations 9.302929 414.1918 at 10iterations 5.386728 144.5575 at 20iterations 3.092045 65.66150 at 30iterations 1.768148 36.57722 at 40iterations 1.005126 22.03063 at 50iterations 0.5732737 11.45470 at 60iterations 0.3265387 6.260458 at 70iterations 0.1853153 3.779045 at 80iterations 0.1049963 2.136219 at 90iterations 5.9672106E-02 1.171000 at 100iterations 3.3837035E-02 0.7224274 at 110iterations 1.9150743E-02 0.3803635 at 120iterations 1.0837389E-02 0.2032385 at 130iterations 6.1578909E-03 0.1252189 at 140iterations 3.4883977E-03 6.7457199E-02 at 150iterations 1.9775892E-03 4.0268898E-02 at 160iterations 1.1220116E-03 2.0864487E-02 at 170iterations 6.3482701E-04 1.2430191E-02 at 180iterations finished qdiffx linear iterations at : 16:33:28 total time elapsed so far: 18.53000 # loops : 180 mean,max change (kT/e) : 6.3482701E-04 1.2430191E-02 energy calculations done at 18.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.68000 DelPhi exited at 16:33:29 18.687u 0.475s 0:19.75 96.9% 0+0k 0+0io 0pf+0w