Mon Oct 10 16:04:41 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 16:04:41 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 = 4310 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: 0.5504275 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): 7.016000 58.63100 ymin,ymax (A): -34.24800 29.88700 zmin,zma (A): -35.35900 29.31800 x,y,z range (A): 51.61500 64.13500 64.67700 scale (grids/A): 0.5504275 object centre (A): 32.82350 -2.180501 -3.020501 number of atom coordinates read : 4310 total number of charged atoms : 4201 net assigned charge : 6.000016 assigned positive charge : 650.9791 centred at (gu) : 89.85690 90.21371 91.46320 assigned negative charge : -644.9823 centred at (gu) : 89.85632 90.26880 91.48117 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8516 nv = 96 ne = 84 npr = 86493 no. pairs analyzed = 86493 no. exposed pairs = 5394 no. arc points = 36898 no. surface atoms = 1808 nbur = 2502 mkacc time = 0.1900000 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= 362 mr = 4612 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 4249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3846 ## 476 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 11353 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5851428E-10 3.4122533E-10 midg,1,midg; midg,igrid,midg 1.0142844E-09 -1.9266461E-10 1,midg,midg; igrid,midg,midg 4.5656892E-10 4.3934975E-10 gauss-seidel spectral radius is 0.9830807 estimated iterations to convergence 63 setup time was (sec) 0.6800000 now iterating at: 16:04:42 rms-change max change #iterations 9.3593106E-02 11.50720 at 10iterations 6.7915535E-03 0.9196339 at 20iterations 8.6404220E-04 0.1729126 at 30iterations 2.7508894E-04 5.0569534E-02 at 40iterations 1.0955789E-04 1.6609192E-02 at 50iterations finished qdiffx linear iterations at : 16:04:45 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 1.0955789E-04 1.6609192E-02 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 16:04:46 4.239u 0.239s 0:05.00 89.2% 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 16:04:46 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 = 4310 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: 1.651282 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): 7.016000 58.63100 ymin,ymax (A): -34.24800 29.88700 zmin,zma (A): -35.35900 29.31800 x,y,z range (A): 51.61500 64.13500 64.67700 scale (grids/A): 1.651282 object centre (A): 32.82350 -2.180501 -3.020501 number of atom coordinates read : 4310 total number of charged atoms : 4201 net assigned charge : 6.000016 assigned positive charge : 650.9791 centred at (gu) : 89.56909 90.63978 94.38832 assigned negative charge : -644.9823 centred at (gu) : 89.56824 90.80592 94.44308 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 95417 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36898 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30745 mr = 67254 m= 3335 mr = 21315 m= 98 mr = 1639 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 39379 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 413 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 32306 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) : 0.5504275 object centre at (A) : 32.82350 -2.180501 -3.020501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7799106E-03 8.7526608E-03 midg,1,midg; midg,igrid,midg 1.9748738E-02 1.4751989E-02 1,midg,midg; igrid,midg,midg 2.5108117E-03 6.3984160E-04 gauss-seidel spectral radius is 0.9983662 estimated iterations to convergence 196 setup time was (sec) 1.100000 now iterating at: 16:04:47 rms-change max change #iterations 4.224505 206.2747 at 10iterations 1.840731 56.35284 at 20iterations 0.8052088 27.69305 at 30iterations 0.3510064 10.44350 at 40iterations 0.1535682 4.807512 at 50iterations 6.7079283E-02 2.000599 at 60iterations 2.9447952E-02 0.8218756 at 70iterations 1.2931666E-02 0.4537430 at 80iterations 5.7162526E-03 0.1887693 at 90iterations 2.5769775E-03 8.5571289E-02 at 100iterations 1.2043421E-03 3.7040710E-02 at 110iterations 6.1091752E-04 1.9943237E-02 at 120iterations finished qdiffx linear iterations at : 16:04:56 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 6.1091752E-04 1.9943237E-02 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.840000 DelPhi exited at 16:04:56 9.838u 0.264s 0:10.53 95.8% 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 16:04:56 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 = 4310 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.476924 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): 7.016000 58.63100 ymin,ymax (A): -34.24800 29.88700 zmin,zma (A): -35.35900 29.31800 x,y,z range (A): 51.61500 64.13500 64.67700 scale (grids/A): 2.476924 object centre (A): 32.82350 -2.180501 -3.020501 number of atom coordinates read : 4310 total number of charged atoms : 4201 net assigned charge : 6.000016 assigned positive charge : 650.9791 centred at (gu) : 89.35320 90.95939 96.58231 assigned negative charge : -644.9823 centred at (gu) : 89.35224 91.20872 96.66460 start vw surface at 0.1900000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 222265 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36898 grid for indexing accessible points = 1.400000 m= 105912 mr = 164582 m= 30962 mr = 84510 m= 5251 mr = 23268 m= 437 mr = 3468 m= 13 mr = 204 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.810000 number of dielectric boundary points 88808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 33574 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) : 1.651282 object centre at (A) : 32.82350 -2.180501 -3.020501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3835728E-02 0.3362037 midg,1,midg; midg,igrid,midg 0.2771251 0.2946809 1,midg,midg; igrid,midg,midg 3.3328161E-02 9.0830904E-03 gauss-seidel spectral radius is 0.9992288 estimated iterations to convergence 284 setup time was (sec) 2.160000 now iterating at: 16:04:59 rms-change max change #iterations 10.83590 315.8853 at 10iterations 6.343952 138.7051 at 20iterations 3.695457 82.67105 at 30iterations 2.140895 45.23010 at 40iterations 1.234932 23.34330 at 50iterations 0.7118863 12.94496 at 60iterations 0.4087059 7.628765 at 70iterations 0.2349308 4.296543 at 80iterations 0.1344794 2.512772 at 90iterations 7.7088267E-02 1.549274 at 100iterations 4.4096027E-02 0.7656193 at 110iterations 2.5151262E-02 0.5641699 at 120iterations 1.4404784E-02 0.2500954 at 130iterations 8.2534393E-03 0.1502724 at 140iterations 4.7417548E-03 9.9552155E-02 at 150iterations 2.7422188E-03 4.8562646E-02 at 160iterations 1.6145116E-03 3.0746460E-02 at 170iterations 9.7214233E-04 1.9325256E-02 at 180iterations finished qdiffx linear iterations at : 16:05:12 total time elapsed so far: 15.58000 # loops : 180 mean,max change (kT/e) : 9.7214233E-04 1.9325256E-02 energy calculations done at 15.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.78000 DelPhi exited at 16:05:13 15.777u 0.256s 0:16.45 97.3% 0+0k 0+0io 0pf+0w