Tue Oct 11 07:52:00 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 07:52:00 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 !!! WARNING: HIR 54 has a net charge of 0.5140 !!! WARNING: HIR 106 has a net charge of 0.5140 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: GLM 208 has a net charge of -0.0940 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: 0.6443672 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): -9.036000 39.85200 ymin,ymax (A): -14.38600 40.86200 zmin,zma (A): 5.247000 52.63900 x,y,z range (A): 48.88800 55.24800 47.39200 scale (grids/A): 0.6443672 object centre (A): 15.40800 13.23800 28.94300 number of atom coordinates read : 2382 total number of charged atoms : 2240 net assigned charge : 3.959008 assigned positive charge : 358.5683 centred at (gu) : 89.44872 88.54705 90.60506 assigned negative charge : -354.6098 centred at (gu) : 89.36050 88.56642 90.77156 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6726 nv = 96 ne = 84 npr = 47807 no. pairs analyzed = 47807 no. exposed pairs = 2869 no. arc points = 20073 no. surface atoms = 966 nbur = 1416 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 3808 m= 2 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3200000 number of dielectric boundary points 3257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2046 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7878 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3078156E-08 -1.5548807E-08 midg,1,midg; midg,igrid,midg 1.2228692E-08 3.2826784E-09 1,midg,midg; igrid,midg,midg -4.5074233E-09 1.5257552E-08 gauss-seidel spectral radius is 0.9875011 estimated iterations to convergence 73 setup time was (sec) 0.6100000 now iterating at: 07:52:01 rms-change max change #iterations 0.1425386 20.07370 at 10iterations 1.4720161E-02 2.084038 at 20iterations 1.6584188E-03 0.2660217 at 30iterations 2.2234111E-04 3.5541534E-02 at 40iterations 3.7531812E-05 6.2980652E-03 at 50iterations finished qdiffx linear iterations at : 07:52:04 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 3.7531812E-05 6.2980652E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 07:52:05 4.107u 0.272s 0:04.84 90.2% 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 07:52:05 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 !!! WARNING: HIR 54 has a net charge of 0.5140 !!! WARNING: HIR 106 has a net charge of 0.5140 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: GLM 208 has a net charge of -0.0940 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: 1.933102 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): -9.036000 39.85200 ymin,ymax (A): -14.38600 40.86200 zmin,zma (A): 5.247000 52.63900 x,y,z range (A): 48.88800 55.24800 47.39200 scale (grids/A): 1.933102 object centre (A): 15.40800 13.23800 28.94300 number of atom coordinates read : 2382 total number of charged atoms : 2240 net assigned charge : 3.959008 assigned positive charge : 358.5683 centred at (gu) : 88.34562 85.64068 91.81459 assigned negative charge : -354.6098 centred at (gu) : 88.08131 85.69921 92.31457 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 72366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20073 grid for indexing accessible points = 1.400000 m= 27445 mr = 50956 m= 4443 mr = 20856 m= 291 mr = 2963 m= 0 mr = 102 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1457 time to turn everything in is 0.6500000 number of dielectric boundary points 29668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17648 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) : 0.6443672 object centre at (A) : 15.40800 13.23800 28.94300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3289129E-02 -2.2642491E-02 midg,1,midg; midg,igrid,midg 2.6580807E-02 1.9645916E-02 1,midg,midg; igrid,midg,midg -5.7378979E-03 4.5503150E-03 gauss-seidel spectral radius is 0.9986514 estimated iterations to convergence 216 setup time was (sec) 0.9600000 now iterating at: 07:52:06 rms-change max change #iterations 4.103920 202.7981 at 10iterations 1.930788 65.17113 at 20iterations 0.9152638 29.64150 at 30iterations 0.4311761 14.64291 at 40iterations 0.2030014 6.626129 at 50iterations 9.5431425E-02 3.296124 at 60iterations 4.5148127E-02 1.368824 at 70iterations 2.1355832E-02 0.7250557 at 80iterations 1.0041457E-02 0.3287849 at 90iterations 4.7485293E-03 0.1580124 at 100iterations 2.2570570E-03 7.2655797E-02 at 110iterations 1.0724062E-03 3.4957528E-02 at 120iterations finished qdiffx linear iterations at : 07:52:14 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 1.0724062E-03 3.4957528E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.570000 DelPhi exited at 07:52:15 9.571u 0.313s 0:10.19 96.9% 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 Tue Oct 11 2011 at 07:52:15 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 !!! WARNING: HIR 54 has a net charge of 0.5140 !!! WARNING: HIR 106 has a net charge of 0.5140 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: GLM 208 has a net charge of -0.0940 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: 2.899652 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): -9.036000 39.85200 ymin,ymax (A): -14.38600 40.86200 zmin,zma (A): 5.247000 52.63900 x,y,z range (A): 48.88800 55.24800 47.39200 scale (grids/A): 2.899652 object centre (A): 15.40800 13.23800 28.94300 number of atom coordinates read : 2382 total number of charged atoms : 2240 net assigned charge : 3.959008 assigned positive charge : 358.5683 centred at (gu) : 87.51846 83.46104 92.72176 assigned negative charge : -354.6098 centred at (gu) : 87.12192 83.54870 93.47191 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 167082 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20073 grid for indexing accessible points = 1.400000 m= 87921 mr = 122929 m= 32773 mr = 73285 m= 8217 mr = 27025 m= 1301 mr = 6315 m= 78 mr = 982 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 5355 time to turn everything in is 1.670000 number of dielectric boundary points 66806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 17917 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) : 1.933102 object centre at (A) : 15.40800 13.23800 28.94300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4794891 -0.3649932 midg,1,midg; midg,igrid,midg 0.1790069 0.1893736 1,midg,midg; igrid,midg,midg -4.1365135E-02 -2.2416694E-02 gauss-seidel spectral radius is 0.9992550 estimated iterations to convergence 289 setup time was (sec) 2.000000 now iterating at: 07:52:17 rms-change max change #iterations 9.652903 395.4551 at 10iterations 5.622732 152.5784 at 20iterations 3.257421 69.72945 at 30iterations 1.888705 37.31973 at 40iterations 1.089901 23.63918 at 50iterations 0.6269429 12.47508 at 60iterations 0.3616059 6.791672 at 70iterations 0.2076302 4.068799 at 80iterations 0.1193974 2.253065 at 90iterations 6.8755560E-02 1.251099 at 100iterations 3.9369114E-02 0.7259197 at 110iterations 2.2672636E-02 0.4249687 at 120iterations 1.3042758E-02 0.2627811 at 130iterations 7.4902177E-03 0.1363220 at 140iterations 4.3174056E-03 8.2167625E-02 at 150iterations 2.5048321E-03 4.4234276E-02 at 160iterations 1.4605130E-03 2.6327133E-02 at 170iterations 8.5901114E-04 1.6010284E-02 at 180iterations finished qdiffx linear iterations at : 07:52:31 total time elapsed so far: 15.96000 # loops : 180 mean,max change (kT/e) : 8.5901114E-04 1.6010284E-02 energy calculations done at 15.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.14000 DelPhi exited at 07:52:32 16.138u 0.328s 0:16.75 98.2% 0+0k 0+0io 0pf+0w