Mon Oct 10 14:04:26 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 14:04:26 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 = 3070 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: 0.6187753 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): -24.19500 33.33800 ymin,ymax (A): 3.639000 51.29800 zmin,zma (A): -27.24200 27.15800 x,y,z range (A): 57.53300 47.65900 54.40000 scale (grids/A): 0.6187753 object centre (A): 4.571501 27.46850 -4.1999817E-02 number of atom coordinates read : 3070 total number of charged atoms : 2931 net assigned charge : -2.499994 assigned positive charge : 449.7993 centred at (gu) : 89.72532 89.52306 90.66599 assigned negative charge : -452.3004 centred at (gu) : 89.73773 89.62662 90.73688 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7999 nv = 96 ne = 84 npr = 62018 no. pairs analyzed = 62018 no. exposed pairs = 3892 no. arc points = 27095 no. surface atoms = 1317 nbur = 1753 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 422 mr = 4464 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2636 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9797 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8465492E-09 -8.4424565E-09 midg,1,midg; midg,igrid,midg 6.3757688E-09 -8.7868841E-09 1,midg,midg; igrid,midg,midg -1.0680165E-09 -2.7004456E-09 gauss-seidel spectral radius is 0.9865187 estimated iterations to convergence 71 setup time was (sec) 0.6400000 now iterating at: 14:04:27 rms-change max change #iterations 0.1341677 20.31378 at 10iterations 1.2658357E-02 1.997066 at 20iterations 1.4644751E-03 0.2009392 at 30iterations 2.6145868E-04 3.8085938E-02 at 40iterations 7.1981493E-05 1.2035370E-02 at 50iterations finished qdiffx linear iterations at : 14:04:31 total time elapsed so far: 4.780000 # loops : 50 mean,max change (kT/e) : 7.1981493E-05 1.2035370E-02 energy calculations done at 4.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.950000 DelPhi exited at 14:04:32 4.958u 0.368s 0:05.66 93.8% 0+0k 0+0io 6pf+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 14:04:32 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 = 3070 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: 1.856326 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): -24.19500 33.33800 ymin,ymax (A): 3.639000 51.29800 zmin,zma (A): -27.24200 27.15800 x,y,z range (A): 57.53300 47.65900 54.40000 scale (grids/A): 1.856326 object centre (A): 4.571501 27.46850 -4.1999817E-02 number of atom coordinates read : 3070 total number of charged atoms : 2931 net assigned charge : -2.499994 assigned positive charge : 449.7993 centred at (gu) : 89.17532 88.56808 91.99703 assigned negative charge : -452.3004 centred at (gu) : 89.21301 88.87962 92.21041 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 87347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27095 grid for indexing accessible points = 1.400000 m= 30993 mr = 61556 m= 4391 mr = 22372 m= 212 mr = 2524 m= 0 mr = 54 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.7000000 number of dielectric boundary points 36437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 22985 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) : 0.6187753 object centre at (A) : 4.571501 27.46850 -4.1999817E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4571634E-04 -3.5058163E-02 midg,1,midg; midg,igrid,midg 1.5649293E-02 -9.1502396E-03 1,midg,midg; igrid,midg,midg -1.1664579E-02 -3.3711076E-02 gauss-seidel spectral radius is 0.9986203 estimated iterations to convergence 213 setup time was (sec) 1.010000 now iterating at: 14:04:33 rms-change max change #iterations 4.356338 164.1091 at 10iterations 2.027784 72.50185 at 20iterations 0.9477860 29.83365 at 30iterations 0.4418346 13.87805 at 40iterations 0.2067897 6.913912 at 50iterations 9.6008159E-02 3.063286 at 60iterations 4.4916682E-02 1.425598 at 70iterations 2.1075780E-02 0.6830826 at 80iterations 9.9060815E-03 0.2888210 at 90iterations 4.6676467E-03 0.1430130 at 100iterations 2.2097477E-03 6.8069220E-02 at 110iterations 1.0598509E-03 3.5985947E-02 at 120iterations finished qdiffx linear iterations at : 14:04:45 total time elapsed so far: 12.61000 # loops : 120 mean,max change (kT/e) : 1.0598509E-03 3.5985947E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 14:04:45 12.784u 0.443s 0:13.66 96.7% 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 14:04:45 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 = 3070 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: 2.784489 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): -24.19500 33.33800 ymin,ymax (A): 3.639000 51.29800 zmin,zma (A): -27.24200 27.15800 x,y,z range (A): 57.53300 47.65900 54.40000 scale (grids/A): 2.784489 object centre (A): 4.571501 27.46850 -4.1999817E-02 number of atom coordinates read : 3070 total number of charged atoms : 2931 net assigned charge : -2.499994 assigned positive charge : 449.7993 centred at (gu) : 88.76280 87.85216 92.99548 assigned negative charge : -452.3004 centred at (gu) : 88.81941 88.31926 93.31567 start vw surface at 0.1200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 202302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27095 grid for indexing accessible points = 1.400000 m= 101552 mr = 149312 m= 35168 mr = 82360 m= 7650 mr = 27648 m= 889 mr = 5381 m= 43 mr = 534 m= 0 mr = 12 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 162 time to turn everything in is 1.830000 number of dielectric boundary points 82357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 23448 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) : 1.856326 object centre at (A) : 4.571501 27.46850 -4.1999817E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1040672 -0.4318677 midg,1,midg; midg,igrid,midg 0.2016301 -6.0632214E-02 1,midg,midg; igrid,midg,midg -0.2260346 -0.5053009 gauss-seidel spectral radius is 0.9992642 estimated iterations to convergence 291 setup time was (sec) 2.190000 now iterating at: 14:04:48 rms-change max change #iterations 10.44825 359.0328 at 10iterations 6.185938 141.3718 at 20iterations 3.637394 81.71082 at 30iterations 2.123271 47.38326 at 40iterations 1.239925 25.12211 at 50iterations 0.7239198 12.91224 at 60iterations 0.4191881 7.764217 at 70iterations 0.2435103 4.339760 at 80iterations 0.1409946 2.588694 at 90iterations 8.1597954E-02 1.485638 at 100iterations 4.7295421E-02 0.9043798 at 110iterations 2.7350733E-02 0.4678459 at 120iterations 1.5869925E-02 0.3245623 at 130iterations 9.2166057E-03 0.1598511 at 140iterations 5.3817751E-03 9.2517853E-02 at 150iterations 3.1602609E-03 6.1113358E-02 at 160iterations 1.8922630E-03 3.6939621E-02 at 170iterations 1.1605284E-03 2.2279739E-02 at 180iterations finished qdiffx linear iterations at : 14:05:06 total time elapsed so far: 20.64000 # loops : 180 mean,max change (kT/e) : 1.1605284E-03 2.2279739E-02 energy calculations done at 20.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.81000 DelPhi exited at 14:05:07 20.810u 0.476s 0:21.80 97.6% 0+0k 0+0io 0pf+0w