Sun Oct 9 20:10:27 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 Sun Oct 9 2011 at 20:10:27 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5294 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5164810 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): 3.304000 68.39400 ymin,ymax (A): -8.981999 52.47100 zmin,zma (A): -1.442000 67.48600 x,y,z range (A): 65.09000 61.45300 68.92800 scale (grids/A): 0.5164810 object centre (A): 35.84900 21.74450 33.02200 number of atom coordinates read : 5294 total number of charged atoms : 5119 net assigned charge : 3.740029 assigned positive charge : 810.6605 centred at (gu) : 88.27235 89.57169 88.79214 assigned negative charge : -806.9265 centred at (gu) : 88.19817 89.59893 88.69519 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9128 nv = 96 ne = 84 npr = 106698 no. pairs analyzed = 106698 no. exposed pairs = 6139 no. arc points = 42001 no. surface atoms = 2083 nbur = 3211 mkacc time = 0.2500000 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 = 1.652000 m= 329 mr = 5161 m= 0 mr = 9 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4214 ## 594 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 12220 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9934192E-10 3.1802197E-10 midg,1,midg; midg,igrid,midg 2.0105147E-10 -2.0789518E-11 1,midg,midg; igrid,midg,midg -3.2196476E-10 2.2518423E-10 gauss-seidel spectral radius is 0.9808602 estimated iterations to convergence 60 setup time was (sec) 0.7700000 now iterating at: 20:10:28 rms-change max change #iterations 8.2704656E-02 12.16354 at 10iterations 1.1439318E-02 1.872360 at 20iterations 4.7702715E-03 0.7599869 at 30iterations 2.2059272E-03 0.3560791 at 40iterations 1.0250864E-03 0.1650925 at 50iterations finished qdiffx linear iterations at : 20:10:31 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 1.0250864E-03 0.1650925 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.840000 DelPhi exited at 20:10:31 3.839u 0.220s 0:04.44 91.2% 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 Sun Oct 9 2011 at 20:10:31 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5294 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.549443 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): 3.304000 68.39400 ymin,ymax (A): -8.981999 52.47100 zmin,zma (A): -1.442000 67.48600 x,y,z range (A): 65.09000 61.45300 68.92800 scale (grids/A): 1.549443 object centre (A): 35.84900 21.74450 33.02200 number of atom coordinates read : 5294 total number of charged atoms : 5119 net assigned charge : 3.740029 assigned positive charge : 810.6605 centred at (gu) : 84.81590 88.71418 86.37487 assigned negative charge : -806.9265 centred at (gu) : 84.59441 88.79655 86.08559 start vw surface at 0.2200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 104236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42001 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 33849 mr = 75430 m= 3339 mr = 24187 m= 55 mr = 1587 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7800000 number of dielectric boundary points 40275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 459 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 38512 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) : 0.5164810 object centre at (A) : 35.84900 21.74450 33.02200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5625734E-02 2.4586316E-02 midg,1,midg; midg,igrid,midg 1.4753223E-02 6.5956260E-03 1,midg,midg; igrid,midg,midg -1.0019113E-02 6.8811147E-05 gauss-seidel spectral radius is 0.9981984 estimated iterations to convergence 187 setup time was (sec) 1.100000 now iterating at: 20:10:33 rms-change max change #iterations 4.187957 175.5413 at 10iterations 1.756422 53.15137 at 20iterations 0.7372496 23.30149 at 30iterations 0.3101002 9.578236 at 40iterations 0.1313629 4.397232 at 50iterations 5.7051778E-02 1.914215 at 60iterations 2.6475735E-02 0.8753548 at 70iterations 1.3972349E-02 0.4685135 at 80iterations 8.7896185E-03 0.3059082 at 90iterations 6.1772806E-03 0.2026520 at 100iterations 4.5759534E-03 0.1505165 at 110iterations 3.4622096E-03 0.1116219 at 120iterations finished qdiffx linear iterations at : 20:10:40 total time elapsed so far: 8.420000 # loops : 120 mean,max change (kT/e) : 3.4622096E-03 0.1116219 energy calculations done at 8.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.620000 DelPhi exited at 20:10:41 8.627u 0.246s 0:09.17 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 Sun Oct 9 2011 at 20:10:41 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5294 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.324164 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): 3.304000 68.39400 ymin,ymax (A): -8.981999 52.47100 zmin,zma (A): -1.442000 67.48600 x,y,z range (A): 65.09000 61.45300 68.92800 scale (grids/A): 2.324164 object centre (A): 35.84900 21.74450 33.02200 number of atom coordinates read : 5294 total number of charged atoms : 5119 net assigned charge : 3.740029 assigned positive charge : 810.6605 centred at (gu) : 82.22334 88.07104 84.56201 assigned negative charge : -806.9265 centred at (gu) : 81.89174 88.19475 84.12823 start vw surface at 0.2200000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 242836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42001 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 118604 mr = 184194 m= 33404 mr = 96062 m= 5004 mr = 25563 m= 306 mr = 3246 m= 5 mr = 152 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.890000 number of dielectric boundary points 90942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 40830 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) : 1.549443 object centre at (A) : 35.84900 21.74450 33.02200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4058299 0.7901187 midg,1,midg; midg,igrid,midg 0.2392775 5.7538178E-02 1,midg,midg; igrid,midg,midg -0.3065461 2.0038910E-02 gauss-seidel spectral radius is 0.9991882 estimated iterations to convergence 277 setup time was (sec) 2.240000 now iterating at: 20:10:43 rms-change max change #iterations 11.02099 322.9916 at 10iterations 6.335664 135.4610 at 20iterations 3.609814 71.76735 at 30iterations 2.048616 39.97198 at 40iterations 1.161207 19.91129 at 50iterations 0.6553819 12.75706 at 60iterations 0.3701557 6.423096 at 70iterations 0.2089016 4.038416 at 80iterations 0.1177477 2.143417 at 90iterations 6.6918015E-02 1.239204 at 100iterations 3.8387489E-02 0.7113533 at 110iterations 2.2512618E-02 0.4245148 at 120iterations 1.3810451E-02 0.2725792 at 130iterations 9.0464354E-03 0.1948776 at 140iterations 6.3954908E-03 0.1278229 at 150iterations 4.8481817E-03 9.4406128E-02 at 160iterations 3.8511991E-03 7.7411652E-02 at 170iterations 3.1473229E-03 6.0516357E-02 at 180iterations finished qdiffx linear iterations at : 20:10:57 total time elapsed so far: 16.12000 # loops : 180 mean,max change (kT/e) : 3.1473229E-03 6.0516357E-02 energy calculations done at 16.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.32000 DelPhi exited at 20:10:57 16.318u 0.258s 0:16.86 98.2% 0+0k 0+0io 0pf+0w