Sat Oct 8 11:44:16 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 11:44:17 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 = 5576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 0.5310025 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): 15.25800 78.55500 ymin,ymax (A): 10.95500 76.69000 zmin,zma (A): 8.405999 75.44901 x,y,z range (A): 63.29700 65.73500 67.04301 scale (grids/A): 0.5310025 object centre (A): 46.90650 43.82250 41.92750 number of atom coordinates read : 5576 total number of charged atoms : 5404 net assigned charge : 1.500026 assigned positive charge : 850.9199 centred at (gu) : 89.74300 90.56958 90.39426 assigned negative charge : -849.4263 centred at (gu) : 89.77613 90.57764 90.42142 start vw surface at 0.2600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 9570 nv = 96 ne = 84 npr = 116192 no. pairs analyzed = 116192 no. exposed pairs = 6629 no. arc points = 45265 no. surface atoms = 2223 nbur = 3353 mkacc time = 0.3500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 369 mr = 5159 m= 0 mr = 13 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 4767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4532 ## 614 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 13154 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2142405E-10 -1.5877452E-10 midg,1,midg; midg,igrid,midg 9.4435119E-11 -7.4069067E-12 1,midg,midg; igrid,midg,midg 3.0662797E-10 -1.7394043E-10 gauss-seidel spectral radius is 0.9819022 estimated iterations to convergence 61 setup time was (sec) 0.9700000 now iterating at: 11:44:18 rms-change max change #iterations 8.9234263E-02 13.31234 at 10iterations 7.2826152E-03 1.264000 at 20iterations 1.3281859E-03 0.3096313 at 30iterations 3.5658310E-04 7.8117371E-02 at 40iterations 1.0470778E-04 2.0469666E-02 at 50iterations finished qdiffx linear iterations at : 11:44:21 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 1.0470778E-04 2.0469666E-02 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 11:44:21 4.332u 0.150s 0:04.76 94.1% 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 11:44:21 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 = 5576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.593007 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): 15.25800 78.55500 ymin,ymax (A): 10.95500 76.69000 zmin,zma (A): 8.405999 75.44901 x,y,z range (A): 63.29700 65.73500 67.04301 scale (grids/A): 1.593007 object centre (A): 46.90650 43.82250 41.92750 number of atom coordinates read : 5576 total number of charged atoms : 5404 net assigned charge : 1.500026 assigned positive charge : 850.9199 centred at (gu) : 89.22687 91.70699 91.18097 assigned negative charge : -849.4263 centred at (gu) : 89.32817 91.73231 91.26413 start vw surface at 0.2600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 109276 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45265 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 32754 mr = 77014 m= 3063 mr = 22334 m= 72 mr = 1407 m= 0 mr = 2 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 733 time to turn everything in is 0.9400000 number of dielectric boundary points 44408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 606 ## 11 charges are in solution ## iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 41116 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) : 0.5310025 object centre at (A) : 46.90650 43.82250 41.92750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0117815E-02 8.9762034E-03 midg,1,midg; midg,igrid,midg 1.2787666E-02 -4.9550883E-03 1,midg,midg; igrid,midg,midg 4.5075198E-03 -6.6610957E-03 gauss-seidel spectral radius is 0.9983287 estimated iterations to convergence 194 setup time was (sec) 1.290000 now iterating at: 11:44:23 rms-change max change #iterations 4.567226 181.2823 at 10iterations 1.976352 59.11210 at 20iterations 0.8524007 24.38097 at 30iterations 0.3696247 10.58514 at 40iterations 0.1605209 4.482117 at 50iterations 6.9438055E-02 1.908524 at 60iterations 3.0236283E-02 0.8248749 at 70iterations 1.3258506E-02 0.4016800 at 80iterations 5.8799284E-03 0.1806679 at 90iterations 2.6450569E-03 9.9044800E-02 at 100iterations 1.2329408E-03 4.6310425E-02 at 110iterations 6.1254331E-04 2.4719238E-02 at 120iterations finished qdiffx linear iterations at : 11:44:31 total time elapsed so far: 9.140000 # loops : 120 mean,max change (kT/e) : 6.1254331E-04 2.4719238E-02 energy calculations done at 9.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 11:44:31 9.393u 0.185s 0:09.85 97.1% 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 11:44:31 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 = 5576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.389511 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): 15.25800 78.55500 ymin,ymax (A): 10.95500 76.69000 zmin,zma (A): 8.405999 75.44901 x,y,z range (A): 63.29700 65.73500 67.04301 scale (grids/A): 2.389511 object centre (A): 46.90650 43.82250 41.92750 number of atom coordinates read : 5576 total number of charged atoms : 5404 net assigned charge : 1.500026 assigned positive charge : 850.9199 centred at (gu) : 88.84003 92.55991 91.77115 assigned negative charge : -849.4263 centred at (gu) : 88.99201 92.59853 91.89629 start vw surface at 0.2800000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 255109 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45265 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 115327 mr = 189237 m= 31195 mr = 90930 m= 4528 mr = 23166 m= 235 mr = 2821 m= 2 mr = 76 m= 2 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.370000 no. cavity mid-points inaccessible to solvent = 2449 time to turn everything in is 2.330000 number of dielectric boundary points 100168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 2.510000 number of grid points assigned charge 43167 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) : 1.593007 object centre at (A) : 46.90650 43.82250 41.92750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2394640 0.1011020 midg,1,midg; midg,igrid,midg 0.1529466 -0.1038190 1,midg,midg; igrid,midg,midg 4.7161631E-02 -0.1805372 gauss-seidel spectral radius is 0.9992377 estimated iterations to convergence 286 setup time was (sec) 2.710000 now iterating at: 11:44:34 rms-change max change #iterations 12.14175 371.3286 at 10iterations 7.207230 161.7712 at 20iterations 4.248431 89.21118 at 30iterations 2.492154 54.12515 at 40iterations 1.453766 28.97008 at 50iterations 0.8435803 18.16705 at 60iterations 0.4898667 8.864296 at 70iterations 0.2833163 5.567725 at 80iterations 0.1634869 3.470097 at 90iterations 9.4194233E-02 1.782590 at 100iterations 5.4280784E-02 1.158199 at 110iterations 3.1257022E-02 0.6764040 at 120iterations 1.8015809E-02 0.3360577 at 130iterations 1.0379187E-02 0.2001820 at 140iterations 5.9960764E-03 0.1144834 at 150iterations 3.4764265E-03 8.2130432E-02 at 160iterations 2.0285223E-03 3.3729553E-02 at 170iterations 1.2012017E-03 2.1356583E-02 at 180iterations finished qdiffx linear iterations at : 11:44:47 total time elapsed so far: 15.27000 # loops : 180 mean,max change (kT/e) : 1.2012017E-03 2.1356583E-02 energy calculations done at 15.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.51000 DelPhi exited at 11:44:47 15.514u 0.185s 0:15.98 98.1% 0+0k 0+0io 0pf+0w