Mon Oct 10 14:04:21 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 Mon Oct 10 2011 at 14:04:21 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: SEP 334 has a net charge of -0.4750 !!! WARNING: ZN5 590 has a net charge of 1.4000 !!! WARNING: ZN5 591 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5780253 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): -2.873000 50.16200 ymin,ymax (A): -7.220000 41.32200 zmin,zma (A): -13.99200 47.59700 x,y,z range (A): 53.03500 48.54200 61.58900 scale (grids/A): 0.5780253 object centre (A): 23.64450 17.05100 16.80250 number of atom coordinates read : 2698 total number of charged atoms : 2555 net assigned charge : 5.864005 assigned positive charge : 413.4046 centred at (gu) : 90.12894 89.55558 88.19627 assigned negative charge : -407.5414 centred at (gu) : 90.09576 89.43668 88.32800 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6101 nv = 96 ne = 84 npr = 53004 no. pairs analyzed = 53004 no. exposed pairs = 3448 no. arc points = 24308 no. surface atoms = 1156 nbur = 1542 mkacc time = 9.0000004E-02 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 = 1.484000 m= 285 mr = 3234 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2409 ## 239 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7538 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5252722E-09 -8.7483937E-10 midg,1,midg; midg,igrid,midg -1.2501594E-09 3.0308471E-09 1,midg,midg; igrid,midg,midg 5.1304844E-10 1.8313970E-09 gauss-seidel spectral radius is 0.9845325 estimated iterations to convergence 66 setup time was (sec) 0.3900000 now iterating at: 14:04:21 rms-change max change #iterations 9.9382415E-02 16.61900 at 10iterations 7.8578750E-03 1.244354 at 20iterations 8.0661016E-04 0.1466579 at 30iterations 1.6792009E-04 4.2663574E-02 at 40iterations 5.2947089E-05 1.3614655E-02 at 50iterations finished qdiffx linear iterations at : 14:04:24 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 5.2947089E-05 1.3614655E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:04:25 3.357u 0.212s 0:04.06 87.6% 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 14:04:25 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: SEP 334 has a net charge of -0.4750 !!! WARNING: ZN5 590 has a net charge of 1.4000 !!! WARNING: ZN5 591 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.734076 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): -2.873000 50.16200 ymin,ymax (A): -7.220000 41.32200 zmin,zma (A): -13.99200 47.59700 x,y,z range (A): 53.03500 48.54200 61.58900 scale (grids/A): 1.734076 object centre (A): 23.64450 17.05100 16.80250 number of atom coordinates read : 2698 total number of charged atoms : 2555 net assigned charge : 5.864005 assigned positive charge : 413.4046 centred at (gu) : 90.38614 88.66616 84.58806 assigned negative charge : -407.5414 centred at (gu) : 90.28702 88.30988 84.98385 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24308 grid for indexing accessible points = 1.400000 m= 22832 mr = 45176 m= 2884 mr = 16207 m= 119 mr = 1587 m= 0 mr = 8 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 433 time to turn everything in is 0.3200000 number of dielectric boundary points 28960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 233 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19811 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) : 0.5780253 object centre at (A) : 23.64450 17.05100 16.80250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7431897E-02 4.7761672E-03 midg,1,midg; midg,igrid,midg -7.2688372E-03 5.2086189E-03 1,midg,midg; igrid,midg,midg -1.4272820E-02 7.9603270E-03 gauss-seidel spectral radius is 0.9983747 estimated iterations to convergence 197 setup time was (sec) 0.5300000 now iterating at: 14:04:25 rms-change max change #iterations 3.641639 159.4405 at 10iterations 1.582614 58.12553 at 20iterations 0.6912149 26.24688 at 30iterations 0.3027029 10.88150 at 40iterations 0.1324842 4.754028 at 50iterations 5.7771046E-02 2.028907 at 60iterations 2.5276544E-02 0.8581104 at 70iterations 1.1192756E-02 0.3791485 at 80iterations 4.9266187E-03 0.1650276 at 90iterations 2.2167091E-03 8.4066391E-02 at 100iterations 1.0331677E-03 3.9970398E-02 at 110iterations 5.1684462E-04 2.2050858E-02 at 120iterations finished qdiffx linear iterations at : 14:04:32 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 5.1684462E-04 2.2050858E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 14:04:33 7.631u 0.214s 0:08.51 92.1% 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 Mon Oct 10 2011 at 14:04:33 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: SEP 334 has a net charge of -0.4750 !!! WARNING: ZN5 590 has a net charge of 1.4000 !!! WARNING: ZN5 591 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.601114 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): -2.873000 50.16200 ymin,ymax (A): -7.220000 41.32200 zmin,zma (A): -13.99200 47.59700 x,y,z range (A): 53.03500 48.54200 61.58900 scale (grids/A): 2.601114 object centre (A): 23.64450 17.05100 16.80250 number of atom coordinates read : 2698 total number of charged atoms : 2555 net assigned charge : 5.864005 assigned positive charge : 413.4046 centred at (gu) : 90.57914 87.99898 81.88198 assigned negative charge : -407.5414 centred at (gu) : 90.43036 87.46482 82.47572 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 152945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24308 grid for indexing accessible points = 1.400000 m= 75579 mr = 109726 m= 24503 mr = 60734 m= 4699 mr = 18899 m= 542 mr = 3299 m= 10 mr = 308 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1376 time to turn everything in is 0.8100000 number of dielectric boundary points 65312 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 20431 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) : 1.734076 object centre at (A) : 23.64450 17.05100 16.80250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.013147 7.3481195E-02 midg,1,midg; midg,igrid,midg -0.1157956 1.4212525E-02 1,midg,midg; igrid,midg,midg -0.2969204 7.4589305E-02 gauss-seidel spectral radius is 0.9991878 estimated iterations to convergence 277 setup time was (sec) 1.050000 now iterating at: 14:04:34 rms-change max change #iterations 9.189501 257.7359 at 10iterations 5.306731 126.6519 at 20iterations 3.045753 69.53912 at 30iterations 1.741182 36.16904 at 40iterations 0.9887278 22.77725 at 50iterations 0.5610724 12.44924 at 60iterations 0.3166992 6.293523 at 70iterations 0.1785505 3.416083 at 80iterations 0.1008546 2.047108 at 90iterations 5.6616638E-02 1.236320 at 100iterations 3.1930640E-02 0.6724167 at 110iterations 1.7950550E-02 0.3553352 at 120iterations 1.0114563E-02 0.1961184 at 130iterations 5.7034604E-03 0.1182377 at 140iterations 3.2342607E-03 6.9324493E-02 at 150iterations 1.8499246E-03 4.2154312E-02 at 160iterations 1.0760013E-03 2.7591705E-02 at 170iterations 6.4567343E-04 1.6246796E-02 at 180iterations finished qdiffx linear iterations at : 14:04:46 total time elapsed so far: 12.14000 # loops : 180 mean,max change (kT/e) : 6.4567343E-04 1.6246796E-02 energy calculations done at 12.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 14:04:46 12.273u 0.199s 0:12.78 97.4% 0+0k 0+0io 0pf+0w