Tue Oct 11 00:13:36 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 Tue Oct 11 2011 at 00:13:36 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2744 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5939570 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): 10.21400 63.97600 ymin,ymax (A): -3.551000 56.38600 zmin,zma (A): 9.639000 52.18100 x,y,z range (A): 53.76200 59.93700 42.54200 scale (grids/A): 0.5939570 object centre (A): 37.09500 26.41750 30.91000 number of atom coordinates read : 2744 total number of charged atoms : 2600 net assigned charge : 6.500019 assigned positive charge : 417.2595 centred at (gu) : 89.12060 91.68931 90.11169 assigned negative charge : -410.7603 centred at (gu) : 89.14740 91.42812 90.25523 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6293 nv = 96 ne = 84 npr = 56099 no. pairs analyzed = 56099 no. exposed pairs = 3202 no. arc points = 22649 no. surface atoms = 1081 nbur = 1663 mkacc time = 9.9999994E-02 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= 285 mr = 3517 m= 0 mr = 20 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 127 time to turn everything in is 0.2000000 number of dielectric boundary points 3041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2309 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4612267E-09 -2.5938454E-09 midg,1,midg; midg,igrid,midg -4.3358788E-09 1.5126988E-08 1,midg,midg; igrid,midg,midg 3.6346866E-09 1.0563299E-09 gauss-seidel spectral radius is 0.9853389 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 00:13:37 rms-change max change #iterations 0.1079330 15.70144 at 10iterations 9.6739270E-03 1.434803 at 20iterations 1.3835069E-03 0.3397789 at 30iterations 3.6900572E-04 9.9018097E-02 at 40iterations 1.0652510E-04 2.9541016E-02 at 50iterations finished qdiffx linear iterations at : 00:13:40 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.0652510E-04 2.9541016E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 00:13:40 3.354u 0.180s 0:04.10 86.0% 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 Tue Oct 11 2011 at 00:13:40 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2744 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.781871 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): 10.21400 63.97600 ymin,ymax (A): -3.551000 56.38600 zmin,zma (A): 9.639000 52.18100 x,y,z range (A): 53.76200 59.93700 42.54200 scale (grids/A): 1.781871 object centre (A): 37.09500 26.41750 30.91000 number of atom coordinates read : 2744 total number of charged atoms : 2600 net assigned charge : 6.500019 assigned positive charge : 417.2595 centred at (gu) : 87.36118 95.06744 90.33429 assigned negative charge : -410.7603 centred at (gu) : 87.44187 94.28397 90.76556 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 69137 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22649 grid for indexing accessible points = 1.400000 m= 23693 mr = 48578 m= 3031 mr = 17548 m= 90 mr = 1813 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 5029 time to turn everything in is 0.3200000 number of dielectric boundary points 27999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20270 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) : 0.5939570 object centre at (A) : 37.09500 26.41750 30.91000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9691121E-02 4.9975323E-03 midg,1,midg; midg,igrid,midg -1.7935568E-02 2.3486655E-02 1,midg,midg; igrid,midg,midg -3.8545632E-03 5.4968391E-03 gauss-seidel spectral radius is 0.9984492 estimated iterations to convergence 201 setup time was (sec) 0.5400000 now iterating at: 00:13:41 rms-change max change #iterations 3.858213 174.9947 at 10iterations 1.710634 68.27692 at 20iterations 0.7607816 24.32793 at 30iterations 0.3405815 11.38869 at 40iterations 0.1522444 4.816713 at 50iterations 6.7979492E-02 2.279556 at 60iterations 3.0386735E-02 0.9678743 at 70iterations 1.3720723E-02 0.4829369 at 80iterations 6.2429756E-03 0.2344246 at 90iterations 2.9154117E-03 0.1127968 at 100iterations 1.4258164E-03 5.8422089E-02 at 110iterations 7.3520554E-04 3.2413483E-02 at 120iterations finished qdiffx linear iterations at : 00:13:48 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 7.3520554E-04 3.2413483E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 00:13:49 7.657u 0.208s 0:08.38 93.6% 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 Tue Oct 11 2011 at 00:13:49 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2744 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.672807 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): 10.21400 63.97600 ymin,ymax (A): -3.551000 56.38600 zmin,zma (A): 9.639000 52.18100 x,y,z range (A): 53.76200 59.93700 42.54200 scale (grids/A): 2.672807 object centre (A): 37.09500 26.41750 30.91000 number of atom coordinates read : 2744 total number of charged atoms : 2600 net assigned charge : 6.500019 assigned positive charge : 417.2595 centred at (gu) : 86.04160 97.60094 90.50141 assigned negative charge : -410.7603 centred at (gu) : 86.16264 96.42592 91.14829 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 160236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22649 grid for indexing accessible points = 1.400000 m= 78802 mr = 117692 m= 26000 mr = 64948 m= 5154 mr = 20782 m= 454 mr = 3744 m= 11 mr = 257 m= 0 mr = 2 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 16921 time to turn everything in is 0.8400000 number of dielectric boundary points 63232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 20790 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) : 1.781871 object centre at (A) : 37.09500 26.41750 30.91000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2169515 6.1858527E-02 midg,1,midg; midg,igrid,midg -0.3221529 -3.7608229E-02 1,midg,midg; igrid,midg,midg -0.1040804 2.7112568E-02 gauss-seidel spectral radius is 0.9992022 estimated iterations to convergence 280 setup time was (sec) 1.070000 now iterating at: 00:13:50 rms-change max change #iterations 9.259783 439.2118 at 10iterations 5.247780 133.9850 at 20iterations 2.959909 61.60295 at 30iterations 1.668527 33.96002 at 40iterations 0.9368292 19.34706 at 50iterations 0.5274375 9.976771 at 60iterations 0.2968481 6.364309 at 70iterations 0.1667575 3.095545 at 80iterations 9.3833007E-02 1.708752 at 90iterations 5.2691273E-02 1.036659 at 100iterations 2.9695602E-02 0.5638628 at 110iterations 1.6743997E-02 0.3164830 at 120iterations 9.4967531E-03 0.2042274 at 130iterations 5.4018651E-03 0.1020203 at 140iterations 3.1069680E-03 6.4809799E-02 at 150iterations 1.8292565E-03 4.2900085E-02 at 160iterations 1.1163561E-03 2.8099060E-02 at 170iterations 7.1107765E-04 1.7913818E-02 at 180iterations finished qdiffx linear iterations at : 00:14:01 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 7.1107765E-04 1.7913818E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.22000 DelPhi exited at 00:14:02 12.218u 0.192s 0:12.84 96.5% 0+0k 0+0io 0pf+0w