Sat Oct 15 14:45:07 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 14:45:07 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2998 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5429147 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): -31.17600 34.39600 ymin,ymax (A): -25.77900 21.20300 zmin,zma (A): -39.78400 6.463000 x,y,z range (A): 65.57200 46.98200 46.24700 scale (grids/A): 0.5429147 object centre (A): 1.610001 -2.287999 -16.66050 number of atom coordinates read : 2998 total number of charged atoms : 2856 net assigned charge : -3.471963 assigned positive charge : 454.3449 centred at (gu) : 90.54601 89.85071 90.58470 assigned negative charge : -457.8181 centred at (gu) : 90.56229 90.00468 90.69138 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5730 nv = 96 ne = 84 npr = 59935 no. pairs analyzed = 59935 no. exposed pairs = 3987 no. arc points = 27713 no. surface atoms = 1332 nbur = 1666 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 = 1.596000 m= 204 mr = 2845 m= 0 mr = 3 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3086 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2777 ## 362 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7509 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9127077E-10 -9.8071895E-10 midg,1,midg; midg,igrid,midg 7.6237872E-10 -1.1025425E-09 1,midg,midg; igrid,midg,midg -7.7830457E-11 -3.2781114E-10 gauss-seidel spectral radius is 0.9825155 estimated iterations to convergence 62 setup time was (sec) 0.6300000 now iterating at: 14:45:08 rms-change max change #iterations 7.3414445E-02 13.77391 at 10iterations 4.7855554E-03 0.7709503 at 20iterations 3.1780402E-04 5.8382988E-02 at 30iterations 2.1148551E-05 3.7403107E-03 at 40iterations 1.4444856E-06 2.3078918E-04 at 50iterations finished qdiffx linear iterations at : 14:45:12 total time elapsed so far: 5.150000 # loops : 50 mean,max change (kT/e) : 1.4444856E-06 2.3078918E-04 energy calculations done at 5.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.320000 DelPhi exited at 14:45:13 5.329u 0.453s 0:06.13 94.1% 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 15 2011 at 14:45:13 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2998 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.628744 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): -31.17600 34.39600 ymin,ymax (A): -25.77900 21.20300 zmin,zma (A): -39.78400 6.463000 x,y,z range (A): 65.57200 46.98200 46.24700 scale (grids/A): 1.628744 object centre (A): 1.610001 -2.287999 -16.66050 number of atom coordinates read : 2998 total number of charged atoms : 2856 net assigned charge : -3.471963 assigned positive charge : 454.3449 centred at (gu) : 91.63733 89.55129 91.75344 assigned negative charge : -457.8181 centred at (gu) : 91.68659 90.01357 92.07348 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27713 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18217 mr = 41744 m= 1791 mr = 12138 m= 39 mr = 845 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 847 time to turn everything in is 0.5300000 number of dielectric boundary points 28584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 329 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21873 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) : 0.5429147 object centre at (A) : 1.610001 -2.287999 -16.66050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1427045E-03 -6.9122096E-03 midg,1,midg; midg,igrid,midg 8.3909007E-03 -1.3743344E-02 1,midg,midg; igrid,midg,midg -3.5691627E-03 -2.4747070E-02 gauss-seidel spectral radius is 0.9981763 estimated iterations to convergence 186 setup time was (sec) 0.8700000 now iterating at: 14:45:14 rms-change max change #iterations 3.353635 158.0344 at 10iterations 1.388303 52.32912 at 20iterations 0.5753862 20.66245 at 30iterations 0.2395906 9.258064 at 40iterations 9.9592738E-02 3.638793 at 50iterations 4.1456696E-02 1.704494 at 60iterations 1.7178757E-02 0.5874500 at 70iterations 7.1499483E-03 0.2800322 at 80iterations 2.9765642E-03 0.1064583 at 90iterations 1.2360892E-03 4.4984818E-02 at 100iterations 5.1415869E-04 1.9557953E-02 at 110iterations 2.1400434E-04 7.5531006E-03 at 120iterations finished qdiffx linear iterations at : 14:45:26 total time elapsed so far: 12.47000 # loops : 120 mean,max change (kT/e) : 2.1400434E-04 7.5531006E-03 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 14:45:27 12.637u 0.539s 0:13.56 97.0% 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 14:45:27 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2998 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.443116 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): -31.17600 34.39600 ymin,ymax (A): -25.77900 21.20300 zmin,zma (A): -39.78400 6.463000 x,y,z range (A): 65.57200 46.98200 46.24700 scale (grids/A): 2.443116 object centre (A): 1.610001 -2.287999 -16.66050 number of atom coordinates read : 2998 total number of charged atoms : 2856 net assigned charge : -3.471963 assigned positive charge : 454.3449 centred at (gu) : 92.45572 89.32671 92.62997 assigned negative charge : -457.8181 centred at (gu) : 92.52975 90.02020 93.11027 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 147270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27713 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 63900 mr = 102863 m= 17205 mr = 49406 m= 2726 mr = 12714 m= 203 mr = 1738 m= 5 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 2946 time to turn everything in is 1.320000 number of dielectric boundary points 64501 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 22814 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) : 1.628744 object centre at (A) : 1.610001 -2.287999 -16.66050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3302519E-03 -8.7672271E-02 midg,1,midg; midg,igrid,midg 0.1422878 -0.1841033 1,midg,midg; igrid,midg,midg 0.2116308 -0.7111513 gauss-seidel spectral radius is 0.9991397 estimated iterations to convergence 269 setup time was (sec) 1.730000 now iterating at: 14:45:29 rms-change max change #iterations 8.777909 371.9138 at 10iterations 4.935465 127.1232 at 20iterations 2.758541 66.35646 at 30iterations 1.531940 41.97675 at 40iterations 0.8512611 19.07494 at 50iterations 0.4698551 9.713272 at 60iterations 0.2592398 5.549682 at 70iterations 0.1429545 3.002834 at 80iterations 7.8631997E-02 1.660452 at 90iterations 4.3322813E-02 0.8718662 at 100iterations 2.3757469E-02 0.5045652 at 110iterations 1.3079524E-02 0.2639732 at 120iterations 7.1851728E-03 0.1618042 at 130iterations 3.9432785E-03 8.3328485E-02 at 140iterations 2.1718389E-03 4.4253349E-02 at 150iterations 1.1935374E-03 2.5672913E-02 at 160iterations 6.5394497E-04 1.3671875E-02 at 170iterations 3.5890538E-04 7.7905655E-03 at 180iterations finished qdiffx linear iterations at : 14:45:48 total time elapsed so far: 20.63000 # loops : 180 mean,max change (kT/e) : 3.5890538E-04 7.7905655E-03 energy calculations done at 20.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.79000 DelPhi exited at 14:45:48 20.797u 0.506s 0:21.62 98.4% 0+0k 0+0io 0pf+0w