Mon Oct 10 10:30:38 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 10:30:38 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 = 2837 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: 0.5607713 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): -20.45700 43.02700 ymin,ymax (A): -9.371000 45.67200 zmin,zma (A): -1.849000 53.17700 x,y,z range (A): 63.48399 55.04300 55.02600 scale (grids/A): 0.5607713 object centre (A): 11.28500 18.15050 25.66400 number of atom coordinates read : 2837 total number of charged atoms : 2686 net assigned charge : 7.500028 assigned positive charge : 413.2299 centred at (gu) : 91.36732 90.53877 86.20428 assigned negative charge : -405.7304 centred at (gu) : 91.51575 90.61576 86.03345 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6063 nv = 96 ne = 84 npr = 54399 no. pairs analyzed = 54399 no. exposed pairs = 4235 no. arc points = 31138 no. surface atoms = 1405 nbur = 1432 mkacc time = 8.9999996E-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 = 1.540000 m= 288 mr = 2684 m= 0 mr = 4 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3064 ## 351 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7709 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3359583E-09 1.0623091E-09 midg,1,midg; midg,igrid,midg 1.4791411E-09 1.3191387E-10 1,midg,midg; igrid,midg,midg 1.7206954E-09 -8.9476115E-10 gauss-seidel spectral radius is 0.9836040 estimated iterations to convergence 64 setup time was (sec) 0.4000000 now iterating at: 10:30:39 rms-change max change #iterations 8.0410488E-02 14.88517 at 10iterations 5.5899625E-03 1.085403 at 20iterations 4.1835071E-04 6.4773560E-02 at 30iterations 3.5831668E-05 5.5961609E-03 at 40iterations 4.9708210E-06 6.2465668E-04 at 50iterations finished qdiffx linear iterations at : 10:30:41 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 4.9708210E-06 6.2465668E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 10:30:42 3.453u 0.167s 0:03.93 91.8% 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 Mon Oct 10 2011 at 10:30:42 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 = 2837 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: 1.682314 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): -20.45700 43.02700 ymin,ymax (A): -9.371000 45.67200 zmin,zma (A): -1.849000 53.17700 x,y,z range (A): 63.48399 55.04300 55.02600 scale (grids/A): 1.682314 object centre (A): 11.28500 18.15050 25.66400 number of atom coordinates read : 2837 total number of charged atoms : 2686 net assigned charge : 7.500028 assigned positive charge : 413.2299 centred at (gu) : 94.10147 91.61587 78.61224 assigned negative charge : -405.7304 centred at (gu) : 94.54699 91.84705 78.10017 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 65415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31138 grid for indexing accessible points = 1.400000 m= 19532 mr = 40056 m= 2176 mr = 12298 m= 73 mr = 906 m= 0 mr = 8 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 33928 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20710 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) : 0.5607713 object centre at (A) : 11.28500 18.15050 25.66400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4055058E-03 8.6798575E-03 midg,1,midg; midg,igrid,midg 1.7887954E-02 2.4562662E-03 1,midg,midg; igrid,midg,midg 1.4075420E-02 -1.5283199E-02 gauss-seidel spectral radius is 0.9982950 estimated iterations to convergence 192 setup time was (sec) 0.5400000 now iterating at: 10:30:43 rms-change max change #iterations 3.372242 142.6578 at 10iterations 1.434985 62.81789 at 20iterations 0.6117476 23.43132 at 30iterations 0.2618288 9.200287 at 40iterations 0.1117742 4.341690 at 50iterations 4.7605779E-02 1.774371 at 60iterations 2.0355588E-02 0.9173393 at 70iterations 8.7024057E-03 0.3332272 at 80iterations 3.7063796E-03 0.1291289 at 90iterations 1.5869190E-03 5.7207108E-02 at 100iterations 6.8095373E-04 2.6855469E-02 at 110iterations 2.9017864E-04 1.0653496E-02 at 120iterations finished qdiffx linear iterations at : 10:30:50 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 2.9017864E-04 1.0653496E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 10:30:50 7.832u 0.211s 0:08.32 96.6% 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 10:30:50 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 = 2837 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: 2.523471 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): -20.45700 43.02700 ymin,ymax (A): -9.371000 45.67200 zmin,zma (A): -1.849000 53.17700 x,y,z range (A): 63.48399 55.04300 55.02600 scale (grids/A): 2.523471 object centre (A): 11.28500 18.15050 25.66400 number of atom coordinates read : 2837 total number of charged atoms : 2686 net assigned charge : 7.500028 assigned positive charge : 413.2299 centred at (gu) : 96.15204 92.42363 72.91829 assigned negative charge : -405.7304 centred at (gu) : 96.82038 92.77051 72.15022 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 151874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31138 grid for indexing accessible points = 1.400000 m= 66055 mr = 99493 m= 19553 mr = 49008 m= 3225 mr = 13930 m= 257 mr = 1874 m= 5 mr = 89 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 76576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21464 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) : 1.682314 object centre at (A) : 11.28500 18.15050 25.66400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4630652E-02 0.1040629 midg,1,midg; midg,igrid,midg 0.3313436 -3.1869885E-02 1,midg,midg; igrid,midg,midg 0.2617745 -0.4659213 gauss-seidel spectral radius is 0.9991798 estimated iterations to convergence 276 setup time was (sec) 1.030000 now iterating at: 10:30:52 rms-change max change #iterations 8.908666 281.4975 at 10iterations 5.183290 150.4853 at 20iterations 2.988484 88.14462 at 30iterations 1.707699 49.63671 at 40iterations 0.9668826 27.80764 at 50iterations 0.5473941 13.67034 at 60iterations 0.3083140 7.522563 at 70iterations 0.1730636 4.255454 at 80iterations 9.7250275E-02 2.383363 at 90iterations 5.4606434E-02 1.288816 at 100iterations 3.0540325E-02 0.7663364 at 110iterations 1.7063612E-02 0.3772807 at 120iterations 9.5400689E-03 0.2316055 at 130iterations 5.3269700E-03 0.1150331 at 140iterations 2.9757821E-03 7.1022034E-02 at 150iterations 1.6602778E-03 3.5995483E-02 at 160iterations 9.2702667E-04 1.8885136E-02 at 170iterations 5.1670551E-04 1.0982513E-02 at 180iterations finished qdiffx linear iterations at : 10:31:03 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 5.1670551E-04 1.0982513E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 10:31:03 12.462u 0.197s 0:12.94 97.7% 0+0k 0+0io 0pf+0w