Sat Oct 8 17:40:04 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 Sat Oct 8 2011 at 17:40:04 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3741 !!! WARNING: ASL 237 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5391979 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): -28.38700 33.46200 ymin,ymax (A): -34.11100 31.91300 zmin,zma (A): 9.104000 63.37600 x,y,z range (A): 61.84900 66.02400 54.27200 scale (grids/A): 0.5391979 object centre (A): 2.537499 -1.099000 36.24000 number of atom coordinates read : 3741 total number of charged atoms : 3592 net assigned charge : -9.099968 assigned positive charge : 575.2996 centred at (gu) : 89.02177 90.30802 90.69048 assigned negative charge : -584.4019 centred at (gu) : 89.07839 90.32246 90.69867 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6831 nv = 96 ne = 84 npr = 76708 no. pairs analyzed = 76708 no. exposed pairs = 4560 no. arc points = 31288 no. surface atoms = 1543 nbur = 2198 mkacc time = 0.2000000 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 = 1.596000 m= 263 mr = 3648 m= 0 mr = 8 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3174 ## 410 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9140 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2247865E-10 -5.8206073E-10 midg,1,midg; midg,igrid,midg -3.1459099E-10 -5.7557809E-10 1,midg,midg; igrid,midg,midg -6.6201662E-11 -6.4464334E-10 gauss-seidel spectral radius is 0.9823220 estimated iterations to convergence 62 setup time was (sec) 0.6900000 now iterating at: 17:40:05 rms-change max change #iterations 8.0761671E-02 13.27927 at 10iterations 5.3426805E-03 1.025311 at 20iterations 3.9657849E-04 6.7206621E-02 at 30iterations 6.3835112E-05 8.9635849E-03 at 40iterations 1.6491202E-05 2.3789406E-03 at 50iterations finished qdiffx linear iterations at : 17:40:09 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 1.6491202E-05 2.3789406E-03 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 17:40:09 4.659u 0.381s 0:05.30 94.9% 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 17:40:09 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3741 !!! WARNING: ASL 237 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.617594 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): -28.38700 33.46200 ymin,ymax (A): -34.11100 31.91300 zmin,zma (A): 9.104000 63.37600 x,y,z range (A): 61.84900 66.02400 54.27200 scale (grids/A): 1.617594 object centre (A): 2.537499 -1.099000 36.24000 number of atom coordinates read : 3741 total number of charged atoms : 3592 net assigned charge : -9.099968 assigned positive charge : 575.2996 centred at (gu) : 87.06402 90.92316 92.07044 assigned negative charge : -584.4019 centred at (gu) : 87.23462 90.96714 92.09569 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31288 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23767 mr = 52924 m= 2339 mr = 16439 m= 56 mr = 1113 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 129 time to turn everything in is 0.6400000 number of dielectric boundary points 32174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 359 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 27384 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) : 0.5391979 object centre at (A) : 2.537499 -1.099000 36.24000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0930544E-03 -7.6633166E-03 midg,1,midg; midg,igrid,midg -2.4100603E-03 -7.7925879E-03 1,midg,midg; igrid,midg,midg -1.7952893E-02 -2.7402468E-02 gauss-seidel spectral radius is 0.9982175 estimated iterations to convergence 188 setup time was (sec) 0.9400000 now iterating at: 17:40:10 rms-change max change #iterations 3.767670 171.0311 at 10iterations 1.585412 68.29663 at 20iterations 0.6651724 21.35871 at 30iterations 0.2803517 8.927271 at 40iterations 0.1174332 4.207588 at 50iterations 4.9641695E-02 1.680058 at 60iterations 2.0887664E-02 0.7366001 at 70iterations 8.8096941E-03 0.2825041 at 80iterations 3.7126348E-03 0.1234398 at 90iterations 1.5711066E-03 5.1086426E-02 at 100iterations 6.6846947E-04 2.1592259E-02 at 110iterations 2.8921390E-04 9.6054077E-03 at 120iterations finished qdiffx linear iterations at : 17:40:20 total time elapsed so far: 10.39000 # loops : 120 mean,max change (kT/e) : 2.8921390E-04 9.6054077E-03 energy calculations done at 10.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.56000 DelPhi exited at 17:40:20 10.563u 0.434s 0:11.25 97.6% 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 Sat Oct 8 2011 at 17:40:20 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3741 !!! WARNING: ASL 237 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.426390 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): -28.38700 33.46200 ymin,ymax (A): -34.11100 31.91300 zmin,zma (A): 9.104000 63.37600 x,y,z range (A): 61.84900 66.02400 54.27200 scale (grids/A): 2.426390 object centre (A): 2.537499 -1.099000 36.24000 number of atom coordinates read : 3741 total number of charged atoms : 3592 net assigned charge : -9.099968 assigned positive charge : 575.2996 centred at (gu) : 85.59579 91.38439 93.10542 assigned negative charge : -584.4019 centred at (gu) : 85.85184 91.45049 93.14349 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 178071 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31288 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 82431 mr = 129664 m= 22997 mr = 65394 m= 3681 mr = 17322 m= 248 mr = 2321 m= 6 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 434 time to turn everything in is 1.570000 number of dielectric boundary points 72628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 28693 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) : 1.617594 object centre at (A) : 2.537499 -1.099000 36.24000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4525595E-02 -0.1379011 midg,1,midg; midg,igrid,midg -1.3657020E-02 -4.6363913E-02 1,midg,midg; igrid,midg,midg -0.3856910 -0.4069007 gauss-seidel spectral radius is 0.9991588 estimated iterations to convergence 272 setup time was (sec) 1.970000 now iterating at: 17:40:23 rms-change max change #iterations 9.838285 309.6425 at 10iterations 5.547048 119.2168 at 20iterations 3.117388 85.73109 at 30iterations 1.747509 32.75651 at 40iterations 0.9726637 18.63558 at 50iterations 0.5425712 12.39733 at 60iterations 0.3018205 5.861995 at 70iterations 0.1674669 3.224438 at 80iterations 9.2833869E-02 1.804694 at 90iterations 5.1542033E-02 1.069605 at 100iterations 2.8595891E-02 0.6270217 at 110iterations 1.5835665E-02 0.2939802 at 120iterations 8.7839775E-03 0.1890483 at 130iterations 4.8647854E-03 9.1426849E-02 at 140iterations 2.6956403E-03 6.5448999E-02 at 150iterations 1.4932281E-03 2.9312134E-02 at 160iterations 8.3084655E-04 1.5033722E-02 at 170iterations 4.6190846E-04 8.6975098E-03 at 180iterations finished qdiffx linear iterations at : 17:40:39 total time elapsed so far: 18.34000 # loops : 180 mean,max change (kT/e) : 4.6190846E-04 8.6975098E-03 energy calculations done at 18.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.52000 DelPhi exited at 17:40:40 18.530u 0.442s 0:19.32 98.1% 0+0k 0+0io 0pf+0w