Tue Oct 11 06:15:49 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 Tue Oct 11 2011 at 06:15:49 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2303 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: ZN7 730 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7325103 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): 25.56600 72.17700 ymin,ymax (A): -18.85400 29.74600 zmin,zma (A): 3.760000 46.13800 x,y,z range (A): 46.61100 48.60000 42.37800 scale (grids/A): 0.7325103 object centre (A): 48.87150 5.446000 24.94900 number of atom coordinates read : 2303 total number of charged atoms : 1981 net assigned charge : 7.600008 assigned positive charge : 322.5839 centred at (gu) : 89.17930 90.77637 90.42648 assigned negative charge : -314.9841 centred at (gu) : 89.32565 90.73849 90.49648 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7760 nv = 96 ne = 84 npr = 42180 no. pairs analyzed = 42180 no. exposed pairs = 2571 no. arc points = 17318 no. surface atoms = 880 nbur = 1423 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 532 mr = 4540 m= 1 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1521 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5901297E-07 5.6108380E-08 midg,1,midg; midg,igrid,midg 6.9795028E-08 1.6729244E-07 1,midg,midg; igrid,midg,midg 2.7570508E-07 -1.1445188E-08 gauss-seidel spectral radius is 0.9902805 estimated iterations to convergence 82 setup time was (sec) 0.5400000 now iterating at: 06:15:49 rms-change max change #iterations 0.2353930 31.24379 at 10iterations 3.0929234E-02 3.943871 at 20iterations 4.1887225E-03 0.5136528 at 30iterations 6.4806157E-04 8.7271452E-02 at 40iterations 1.4215578E-04 1.7164707E-02 at 50iterations finished qdiffx linear iterations at : 06:15:53 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 1.4215578E-04 1.7164707E-02 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 06:15:53 4.111u 0.246s 0:04.72 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 Tue Oct 11 2011 at 06:15:53 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2303 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: ZN7 730 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.197531 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): 25.56600 72.17700 ymin,ymax (A): -18.85400 29.74600 zmin,zma (A): 3.760000 46.13800 x,y,z range (A): 46.61100 48.60000 42.37800 scale (grids/A): 2.197531 object centre (A): 48.87150 5.446000 24.94900 number of atom coordinates read : 2303 total number of charged atoms : 1981 net assigned charge : 7.600008 assigned positive charge : 322.5839 centred at (gu) : 87.53790 92.32880 91.27953 assigned negative charge : -314.9841 centred at (gu) : 87.97695 92.21563 91.48949 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81383 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17318 grid for indexing accessible points = 1.400000 m= 34175 mr = 58436 m= 7133 mr = 26450 m= 702 mr = 4868 m= 26 mr = 370 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 33295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15745 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) : 0.7325103 object centre at (A) : 48.87150 5.446000 24.94900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8878761E-02 3.7498873E-02 midg,1,midg; midg,igrid,midg 5.6380078E-02 4.2580362E-02 1,midg,midg; igrid,midg,midg 6.0806576E-02 -5.8931462E-02 gauss-seidel spectral radius is 0.9988984 estimated iterations to convergence 238 setup time was (sec) 0.9700000 now iterating at: 06:15:55 rms-change max change #iterations 4.927968 184.7072 at 10iterations 2.491741 80.63419 at 20iterations 1.266154 36.94558 at 30iterations 0.6394118 19.60823 at 40iterations 0.3236919 9.776483 at 50iterations 0.1645972 4.771098 at 60iterations 8.3373137E-02 2.418566 at 70iterations 4.2381454E-02 1.146179 at 80iterations 2.1549193E-02 0.5729307 at 90iterations 1.0977725E-02 0.3217819 at 100iterations 5.6141261E-03 0.1635590 at 110iterations 2.9069674E-03 8.6006105E-02 at 120iterations finished qdiffx linear iterations at : 06:16:03 total time elapsed so far: 9.360000 # loops : 120 mean,max change (kT/e) : 2.9069674E-03 8.6006105E-02 energy calculations done at 9.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 06:16:04 9.537u 0.260s 0:10.11 96.8% 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 Tue Oct 11 2011 at 06:16:04 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2303 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: ZN7 730 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.296296 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): 25.56600 72.17700 ymin,ymax (A): -18.85400 29.74600 zmin,zma (A): 3.760000 46.13800 x,y,z range (A): 46.61100 48.60000 42.37800 scale (grids/A): 3.296296 object centre (A): 48.87150 5.446000 24.94900 number of atom coordinates read : 2303 total number of charged atoms : 1981 net assigned charge : 7.600008 assigned positive charge : 322.5839 centred at (gu) : 86.30677 93.49337 91.91922 assigned negative charge : -314.9841 centred at (gu) : 86.96547 93.32333 92.23430 start vw surface at 0.1400000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 187319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17318 grid for indexing accessible points = 1.400000 m= 104672 mr = 140297 m= 45023 mr = 87924 m= 13720 mr = 37444 m= 2854 mr = 10767 m= 432 mr = 2101 m= 33 mr = 291 m= 0 mr = 9 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.090000 number of dielectric boundary points 75220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 15848 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) : 2.197531 object centre at (A) : 48.87150 5.446000 24.94900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1449418 0.3243349 midg,1,midg; midg,igrid,midg 0.4323577 0.2217352 1,midg,midg; igrid,midg,midg 0.5447367 -0.6703030 gauss-seidel spectral radius is 0.9993141 estimated iterations to convergence 301 setup time was (sec) 2.420000 now iterating at: 06:16:06 rms-change max change #iterations 10.82598 294.7226 at 10iterations 6.457579 135.4445 at 20iterations 3.847152 80.96078 at 30iterations 2.291706 46.12851 at 40iterations 1.359985 26.59718 at 50iterations 0.8061492 16.66697 at 60iterations 0.4770376 9.504396 at 70iterations 0.2821052 4.936943 at 80iterations 0.1665398 3.341685 at 90iterations 9.8322362E-02 1.661791 at 100iterations 5.8154784E-02 0.9495773 at 110iterations 3.4494638E-02 0.5897827 at 120iterations 2.0487493E-02 0.3349791 at 130iterations 1.2333547E-02 0.2147179 at 140iterations 7.5613759E-03 0.1298523 at 150iterations 4.7824727E-03 8.9805603E-02 at 160iterations 3.1704453E-03 5.8872223E-02 at 170iterations 2.2400308E-03 4.2181015E-02 at 180iterations finished qdiffx linear iterations at : 06:16:20 total time elapsed so far: 15.73000 # loops : 180 mean,max change (kT/e) : 2.2400308E-03 4.2181015E-02 energy calculations done at 15.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.91000 DelPhi exited at 06:16:20 15.911u 0.270s 0:16.47 98.2% 0+0k 0+0io 0pf+0w