Sun Oct 9 09:41:32 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 Sun Oct 9 2011 at 09:41:32 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 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: 0.6082455 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): -5.624000 46.76500 ymin,ymax (A): 16.33800 67.79000 zmin,zma (A): 62.73400 121.2630 x,y,z range (A): 52.38900 51.45200 58.52900 scale (grids/A): 0.6082455 object centre (A): 20.57050 42.06400 91.99850 number of atom coordinates read : 2571 total number of charged atoms : 2431 net assigned charge : 6.000026 assigned positive charge : 379.7930 centred at (gu) : 88.76673 89.77887 89.57430 assigned negative charge : -373.7935 centred at (gu) : 88.73190 89.86251 89.50235 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6467 nv = 96 ne = 84 npr = 51548 no. pairs analyzed = 51548 no. exposed pairs = 3328 no. arc points = 23846 no. surface atoms = 1114 nbur = 1457 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 302 mr = 3316 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2442 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7962 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.2417712E-11 6.0035967E-09 midg,1,midg; midg,igrid,midg 7.4768014E-09 -4.0643183E-10 1,midg,midg; igrid,midg,midg 2.3225410E-09 3.7733616E-09 gauss-seidel spectral radius is 0.9860137 estimated iterations to convergence 69 setup time was (sec) 0.5100000 now iterating at: 09:41:33 rms-change max change #iterations 0.1155756 18.10131 at 10iterations 1.0223968E-02 1.957640 at 20iterations 8.9652144E-04 0.1450272 at 30iterations 7.8925237E-05 1.0711670E-02 at 40iterations 7.0798660E-06 1.0359287E-03 at 50iterations finished qdiffx linear iterations at : 09:41:36 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 7.0798660E-06 1.0359287E-03 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 09:41:36 3.289u 0.188s 0:03.76 92.0% 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 Sun Oct 9 2011 at 09:41:36 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.824736 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): -5.624000 46.76500 ymin,ymax (A): 16.33800 67.79000 zmin,zma (A): 62.73400 121.2630 x,y,z range (A): 52.38900 51.45200 58.52900 scale (grids/A): 1.824736 object centre (A): 20.57050 42.06400 91.99850 number of atom coordinates read : 2571 total number of charged atoms : 2431 net assigned charge : 6.000026 assigned positive charge : 379.7930 centred at (gu) : 86.29964 89.33627 88.72241 assigned negative charge : -373.7935 centred at (gu) : 86.19520 89.58740 88.50690 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70050 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23846 grid for indexing accessible points = 1.400000 m= 24012 mr = 47029 m= 3358 mr = 16955 m= 175 mr = 1758 m= 0 mr = 47 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 31806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19019 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) : 0.6082455 object centre at (A) : 20.57050 42.06400 91.99850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8751999E-02 1.2169974E-02 midg,1,midg; midg,igrid,midg 3.4079436E-02 1.5199878E-03 1,midg,midg; igrid,midg,midg -1.2380150E-02 1.4928165E-02 gauss-seidel spectral radius is 0.9985256 estimated iterations to convergence 207 setup time was (sec) 0.7800000 now iterating at: 09:41:37 rms-change max change #iterations 3.880898 170.8312 at 10iterations 1.764068 65.65363 at 20iterations 0.7982859 28.14131 at 30iterations 0.3627274 11.53573 at 40iterations 0.1642961 5.112588 at 50iterations 7.4622944E-02 2.621541 at 60iterations 3.3971149E-02 1.140641 at 70iterations 1.5342329E-02 0.5545962 at 80iterations 7.0033199E-03 0.2626305 at 90iterations 3.1747597E-03 0.1060281 at 100iterations 1.4386795E-03 4.8853397E-02 at 110iterations 6.5363175E-04 2.2541046E-02 at 120iterations finished qdiffx linear iterations at : 09:41:44 total time elapsed so far: 7.200000 # loops : 120 mean,max change (kT/e) : 6.5363175E-04 2.2541046E-02 energy calculations done at 7.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.370000 DelPhi exited at 09:41:44 7.368u 0.226s 0:07.92 95.7% 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 Sun Oct 9 2011 at 09:41:44 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.737105 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): -5.624000 46.76500 ymin,ymax (A): 16.33800 67.79000 zmin,zma (A): 62.73400 121.2630 x,y,z range (A): 52.38900 51.45200 58.52900 scale (grids/A): 2.737105 object centre (A): 20.57050 42.06400 91.99850 number of atom coordinates read : 2571 total number of charged atoms : 2431 net assigned charge : 6.000026 assigned positive charge : 379.7930 centred at (gu) : 84.44936 89.00419 88.08353 assigned negative charge : -373.7935 centred at (gu) : 84.29275 89.38098 87.76027 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 162141 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23846 grid for indexing accessible points = 1.400000 m= 78458 mr = 114777 m= 26633 mr = 62357 m= 5559 mr = 20491 m= 706 mr = 3744 m= 21 mr = 411 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 71736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 19439 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) : 1.824736 object centre at (A) : 20.57050 42.06400 91.99850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4825446 2.8318031E-02 midg,1,midg; midg,igrid,midg 0.3405952 -2.2004047E-02 1,midg,midg; igrid,midg,midg -0.2402248 0.1479636 gauss-seidel spectral radius is 0.9992350 estimated iterations to convergence 285 setup time was (sec) 1.550000 now iterating at: 09:41:46 rms-change max change #iterations 9.444290 327.0555 at 10iterations 5.539388 141.5183 at 20iterations 3.211019 75.93826 at 30iterations 1.851920 42.10974 at 40iterations 1.066221 21.12376 at 50iterations 0.6108794 13.63475 at 60iterations 0.3494793 7.360918 at 70iterations 0.1998426 4.319134 at 80iterations 0.1141304 2.293667 at 90iterations 6.5035217E-02 1.306324 at 100iterations 3.7166342E-02 0.7528267 at 110iterations 2.1111296E-02 0.4198723 at 120iterations 1.2040301E-02 0.2304459 at 130iterations 6.8482100E-03 0.1440430 at 140iterations 3.8990318E-03 8.8522911E-02 at 150iterations 2.2191678E-03 4.5309544E-02 at 160iterations 1.2658306E-03 2.5083542E-02 at 170iterations 7.2202779E-04 1.3114929E-02 at 180iterations finished qdiffx linear iterations at : 09:41:56 total time elapsed so far: 11.97000 # loops : 180 mean,max change (kT/e) : 7.2202779E-04 1.3114929E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 09:41:57 12.147u 0.219s 0:12.66 97.5% 0+0k 0+0io 0pf+0w