Sat Oct 8 15:57:39 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 Sat Oct 8 2011 at 15:57:39 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 = 2321 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: 0.6479089 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): 24.76100 72.75400 ymin,ymax (A): -17.39800 29.30800 zmin,zma (A): -18.56500 36.38100 x,y,z range (A): 47.99300 46.70600 54.94600 scale (grids/A): 0.6479089 object centre (A): 48.75750 5.955000 8.907998 number of atom coordinates read : 2321 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 90.53290 89.13052 90.24591 assigned negative charge : -338.3788 centred at (gu) : 90.59320 89.24103 90.28330 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6548 nv = 96 ne = 84 npr = 47538 no. pairs analyzed = 47538 no. exposed pairs = 2812 no. arc points = 19541 no. surface atoms = 964 nbur = 1357 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3656 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3000000 number of dielectric boundary points 3178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1888 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7857 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1306050E-08 2.6086757E-09 midg,1,midg; midg,igrid,midg 2.5211078E-08 -5.6187863E-09 1,midg,midg; igrid,midg,midg 1.3194004E-08 -5.2007959E-10 gauss-seidel spectral radius is 0.9876300 estimated iterations to convergence 73 setup time was (sec) 0.6100000 now iterating at: 15:57:39 rms-change max change #iterations 0.1440183 20.63173 at 10iterations 1.4536751E-02 2.326943 at 20iterations 1.5148055E-03 0.2358990 at 30iterations 1.6993879E-04 2.4593353E-02 at 40iterations 2.4049305E-05 4.1296482E-03 at 50iterations finished qdiffx linear iterations at : 15:57:43 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 2.4049305E-05 4.1296482E-03 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 15:57:44 4.500u 0.374s 0:05.19 93.8% 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 8 2011 at 15:57:44 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 = 2321 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: 1.943727 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): 24.76100 72.75400 ymin,ymax (A): -17.39800 29.30800 zmin,zma (A): -18.56500 36.38100 x,y,z range (A): 47.99300 46.70600 54.94600 scale (grids/A): 1.943727 object centre (A): 48.75750 5.955000 8.907998 number of atom coordinates read : 2321 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 91.59789 87.39117 90.73750 assigned negative charge : -338.3788 centred at (gu) : 91.77949 87.72296 90.84990 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70565 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19541 grid for indexing accessible points = 1.400000 m= 25103 mr = 49511 m= 4148 mr = 18600 m= 249 mr = 2712 m= 6 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 902 time to turn everything in is 0.5800000 number of dielectric boundary points 29144 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17603 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) : 0.6479089 object centre at (A) : 48.75750 5.955000 8.907998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0916408E-02 -1.6861273E-02 midg,1,midg; midg,igrid,midg 2.4805399E-02 -4.3287924E-03 1,midg,midg; igrid,midg,midg 9.2145791E-03 -4.1799065E-02 gauss-seidel spectral radius is 0.9986572 estimated iterations to convergence 216 setup time was (sec) 0.8700000 now iterating at: 15:57:45 rms-change max change #iterations 4.094219 175.9604 at 10iterations 1.927532 72.19906 at 20iterations 0.9110486 32.99336 at 30iterations 0.4299473 13.90839 at 40iterations 0.2028584 6.321010 at 50iterations 9.5494494E-02 3.051583 at 60iterations 4.5013782E-02 1.508634 at 70iterations 2.1298449E-02 0.7139375 at 80iterations 1.0016060E-02 0.3228521 at 90iterations 4.7420184E-03 0.1444417 at 100iterations 2.2292379E-03 6.9294989E-02 at 110iterations 1.0558096E-03 3.1867027E-02 at 120iterations finished qdiffx linear iterations at : 15:57:55 total time elapsed so far: 10.39000 # loops : 120 mean,max change (kT/e) : 1.0558096E-03 3.1867027E-02 energy calculations done at 10.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.57000 DelPhi exited at 15:57:55 10.570u 0.445s 0:11.43 96.3% 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 8 2011 at 15:57:55 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 = 2321 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: 2.915590 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): 24.76100 72.75400 ymin,ymax (A): -17.39800 29.30800 zmin,zma (A): -18.56500 36.38100 x,y,z range (A): 47.99300 46.70600 54.94600 scale (grids/A): 2.915590 object centre (A): 48.75750 5.955000 8.907998 number of atom coordinates read : 2321 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 92.39675 86.08670 91.10624 assigned negative charge : -338.3788 centred at (gu) : 92.66920 86.58444 91.27489 start vw surface at 0.1200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 163340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19541 grid for indexing accessible points = 1.400000 m= 81155 mr = 119929 m= 29535 mr = 66548 m= 7775 mr = 23966 m= 1158 mr = 6041 m= 65 mr = 794 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 3039 time to turn everything in is 1.510000 number of dielectric boundary points 65722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 17839 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) : 1.943727 object centre at (A) : 48.75750 5.955000 8.907998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1928711 -0.2304429 midg,1,midg; midg,igrid,midg 0.1925437 -6.6743828E-02 1,midg,midg; igrid,midg,midg 9.6571416E-02 -0.5801173 gauss-seidel spectral radius is 0.9992592 estimated iterations to convergence 290 setup time was (sec) 1.860000 now iterating at: 15:57:58 rms-change max change #iterations 9.522523 480.2895 at 10iterations 5.542858 116.6238 at 20iterations 3.216160 68.87203 at 30iterations 1.862265 39.86560 at 40iterations 1.077685 22.46082 at 50iterations 0.6225617 11.38181 at 60iterations 0.3588509 6.501831 at 70iterations 0.2067436 4.072657 at 80iterations 0.1191265 2.323696 at 90iterations 6.8627365E-02 1.309172 at 100iterations 3.9468620E-02 0.7194796 at 110iterations 2.2674102E-02 0.4556160 at 120iterations 1.3069468E-02 0.2422466 at 130iterations 7.5075738E-03 0.1466675 at 140iterations 4.3245265E-03 8.0184937E-02 at 150iterations 2.4892585E-03 4.5047760E-02 at 160iterations 1.4372456E-03 2.6643753E-02 at 170iterations 8.3140552E-04 1.7425537E-02 at 180iterations finished qdiffx linear iterations at : 15:58:14 total time elapsed so far: 18.25000 # loops : 180 mean,max change (kT/e) : 8.3140552E-04 1.7425537E-02 energy calculations done at 18.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.41000 DelPhi exited at 15:58:14 18.420u 0.425s 0:19.13 98.4% 0+0k 0+0io 0pf+0w