Mon Oct 10 17:03:10 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 17:03:10 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 = 2818 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: 0.6056997 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): 13.24300 72.01800 ymin,ymax (A): 3.629000 50.11200 zmin,zma (A): 7.469000 63.12600 x,y,z range (A): 58.77500 46.48300 55.65700 scale (grids/A): 0.6056997 object centre (A): 42.63050 26.87050 35.29750 number of atom coordinates read : 2818 total number of charged atoms : 2677 net assigned charge : -0.9999679 assigned positive charge : 424.0082 centred at (gu) : 88.60619 90.20993 90.95049 assigned negative charge : -425.0093 centred at (gu) : 88.50878 90.30070 90.98392 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6834 nv = 96 ne = 84 npr = 56243 no. pairs analyzed = 56243 no. exposed pairs = 3779 no. arc points = 26780 no. surface atoms = 1270 nbur = 1548 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3452 m= 0 mr = 34 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2722 ## 299 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8569 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3790864E-10 -2.4851441E-09 midg,1,midg; midg,igrid,midg 3.6704386E-09 -4.9948090E-09 1,midg,midg; igrid,midg,midg -7.0062725E-09 3.0250276E-09 gauss-seidel spectral radius is 0.9859149 estimated iterations to convergence 69 setup time was (sec) 0.7700000 now iterating at: 17:03:11 rms-change max change #iterations 0.1195886 18.29173 at 10iterations 1.0235985E-02 1.621353 at 20iterations 8.8709040E-04 0.1361771 at 30iterations 7.8245830E-05 1.3284683E-02 at 40iterations 7.4893305E-06 1.2512207E-03 at 50iterations finished qdiffx linear iterations at : 17:03:18 total time elapsed so far: 6.910000 # loops : 50 mean,max change (kT/e) : 7.4893305E-06 1.2512207E-03 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 17:03:19 7.077u 0.640s 0:09.26 83.2% 0+0k 0+0io 3pf+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 17:03:19 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 = 2818 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: 1.817099 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): 13.24300 72.01800 ymin,ymax (A): 3.629000 50.11200 zmin,zma (A): 7.469000 63.12600 x,y,z range (A): 58.77500 46.48300 55.65700 scale (grids/A): 1.817099 object centre (A): 42.63050 26.87050 35.29750 number of atom coordinates read : 2818 total number of charged atoms : 2677 net assigned charge : -0.9999679 assigned positive charge : 424.0082 centred at (gu) : 85.81787 90.62912 92.85069 assigned negative charge : -425.0093 centred at (gu) : 85.52622 90.90204 92.95123 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26780 grid for indexing accessible points = 1.400000 m= 24456 mr = 48862 m= 3400 mr = 17001 m= 169 mr = 1871 m= 4 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 34157 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 20899 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) : 0.6056997 object centre at (A) : 42.63050 26.87050 35.29750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9282046E-03 6.1981627E-03 midg,1,midg; midg,igrid,midg 1.1055467E-02 -1.2621297E-02 1,midg,midg; igrid,midg,midg -5.1368795E-02 1.6974589E-02 gauss-seidel spectral radius is 0.9985342 estimated iterations to convergence 207 setup time was (sec) 1.220000 now iterating at: 17:03:21 rms-change max change #iterations 4.078801 160.6640 at 10iterations 1.851377 68.91092 at 20iterations 0.8376464 31.85415 at 30iterations 0.3810880 12.05611 at 40iterations 0.1730899 6.075390 at 50iterations 7.8737408E-02 2.548760 at 60iterations 3.5686519E-02 1.177917 at 70iterations 1.6280331E-02 0.5268478 at 80iterations 7.4103363E-03 0.2392495 at 90iterations 3.3630652E-03 0.1168938 at 100iterations 1.5373771E-03 5.0736070E-02 at 110iterations 6.9861196E-04 2.1206856E-02 at 120iterations finished qdiffx linear iterations at : 17:03:37 total time elapsed so far: 16.59000 # loops : 120 mean,max change (kT/e) : 6.9861196E-04 2.1206856E-02 energy calculations done at 16.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.78000 DelPhi exited at 17:03:38 16.787u 0.695s 0:18.97 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 Mon Oct 10 2011 at 17:03:39 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 = 2818 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: 2.725649 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): 13.24300 72.01800 ymin,ymax (A): 3.629000 50.11200 zmin,zma (A): 7.469000 63.12600 x,y,z range (A): 58.77500 46.48300 55.65700 scale (grids/A): 2.725649 object centre (A): 42.63050 26.87050 35.29750 number of atom coordinates read : 2818 total number of charged atoms : 2677 net assigned charge : -0.9999679 assigned positive charge : 424.0082 centred at (gu) : 83.72657 90.94359 94.27575 assigned negative charge : -425.0093 centred at (gu) : 83.28941 91.35294 94.42684 start vw surface at 0.1200000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 171101 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26780 grid for indexing accessible points = 1.400000 m= 80661 mr = 119265 m= 26854 mr = 63692 m= 5823 mr = 20520 m= 749 mr = 4165 m= 41 mr = 462 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.750000 number of dielectric boundary points 77114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 21414 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) : 1.817099 object centre at (A) : 42.63050 26.87050 35.29750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9535912E-02 0.1439425 midg,1,midg; midg,igrid,midg 0.1161030 -0.1199599 1,midg,midg; igrid,midg,midg -0.6606476 0.2155861 gauss-seidel spectral radius is 0.9992498 estimated iterations to convergence 288 setup time was (sec) 2.310000 now iterating at: 17:03:42 rms-change max change #iterations 10.00619 298.1741 at 10iterations 5.903451 137.0366 at 20iterations 3.461349 75.05611 at 30iterations 2.005150 48.59582 at 40iterations 1.163455 23.02170 at 50iterations 0.6711533 14.24351 at 60iterations 0.3878619 7.837057 at 70iterations 0.2227194 4.319328 at 80iterations 0.1275856 2.619316 at 90iterations 7.3392309E-02 1.401112 at 100iterations 4.2041562E-02 0.8318710 at 110iterations 2.4142368E-02 0.4836020 at 120iterations 1.3797392E-02 0.2868309 at 130iterations 7.9221763E-03 0.1435089 at 140iterations 4.5333216E-03 9.0846062E-02 at 150iterations 2.5901913E-03 4.7712326E-02 at 160iterations 1.4839009E-03 2.7633667E-02 at 170iterations 8.4983936E-04 1.5951157E-02 at 180iterations finished qdiffx linear iterations at : 17:04:09 total time elapsed so far: 28.61000 # loops : 180 mean,max change (kT/e) : 8.4983936E-04 1.5951157E-02 energy calculations done at 28.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 28.79000 DelPhi exited at 17:04:10 28.792u 0.775s 0:30.41 97.2% 0+0k 0+0io 0pf+0w