Mon Oct 10 13:59:23 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 Mon Oct 10 2011 at 13:59:24 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4244 !!! WARNING: HIR 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5848145 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): -25.79100 35.08300 ymin,ymax (A): 34.85500 92.30099 zmin,zma (A): 30.66900 89.29600 x,y,z range (A): 60.87400 57.44599 58.62700 scale (grids/A): 0.5848145 object centre (A): 4.646000 63.57800 59.98250 number of atom coordinates read : 4244 total number of charged atoms : 4108 net assigned charge : -0.9859585 assigned positive charge : 641.3665 centred at (gu) : 91.20721 89.56634 88.66151 assigned negative charge : -642.3555 centred at (gu) : 91.05048 89.69317 88.84888 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9168 nv = 96 ne = 84 npr = 89933 no. pairs analyzed = 89933 no. exposed pairs = 4696 no. arc points = 31647 no. surface atoms = 1609 nbur = 2635 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 = 1.484000 m= 401 mr = 5392 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 221 time to turn everything in is 0.5000000 number of dielectric boundary points 4136 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3275 ## 372 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12128 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7694216E-09 -5.5290559E-09 midg,1,midg; midg,igrid,midg 4.6569504E-09 -4.7240705E-09 1,midg,midg; igrid,midg,midg -4.8072235E-09 7.0380128E-09 gauss-seidel spectral radius is 0.9849927 estimated iterations to convergence 67 setup time was (sec) 0.7700000 now iterating at: 13:59:25 rms-change max change #iterations 0.1268032 16.19167 at 10iterations 1.0411069E-02 1.411833 at 20iterations 9.8528760E-04 0.1340237 at 30iterations 1.7312655E-04 2.4092481E-02 at 40iterations 5.1139352E-05 7.6253563E-03 at 50iterations finished qdiffx linear iterations at : 13:59:28 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 5.1139352E-05 7.6253563E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 13:59:29 4.249u 0.259s 0:05.39 83.3% 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 13:59:29 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4244 !!! WARNING: HIR 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.754444 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): -25.79100 35.08300 ymin,ymax (A): 34.85500 92.30099 zmin,zma (A): 30.66900 89.29600 x,y,z range (A): 60.87400 57.44599 58.62700 scale (grids/A): 1.754444 object centre (A): 4.646000 63.57800 59.98250 number of atom coordinates read : 4244 total number of charged atoms : 4108 net assigned charge : -0.9859585 assigned positive charge : 641.3665 centred at (gu) : 93.62034 88.69779 85.98335 assigned negative charge : -642.3555 centred at (gu) : 93.15089 89.07909 86.54611 start vw surface at 0.1900000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 102384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31647 grid for indexing accessible points = 1.400000 m= 35207 mr = 74860 m= 4795 mr = 26324 m= 180 mr = 3021 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 7468 time to turn everything in is 0.8700000 number of dielectric boundary points 38304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 288 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 31962 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) : 0.5848145 object centre at (A) : 4.646000 63.57800 59.98250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3877600E-02 -3.3824250E-02 midg,1,midg; midg,igrid,midg 2.4428746E-02 -2.8860249E-02 1,midg,midg; igrid,midg,midg -1.1536275E-02 4.7965974E-02 gauss-seidel spectral radius is 0.9985363 estimated iterations to convergence 207 setup time was (sec) 1.170000 now iterating at: 13:59:31 rms-change max change #iterations 4.830421 170.0586 at 10iterations 2.199347 68.70724 at 20iterations 1.001868 30.92895 at 30iterations 0.4568119 13.29418 at 40iterations 0.2095603 5.897434 at 50iterations 9.5692344E-02 2.563048 at 60iterations 4.3774433E-02 1.145777 at 70iterations 2.0040844E-02 0.5899668 at 80iterations 9.1742743E-03 0.2577648 at 90iterations 4.2134007E-03 0.1147709 at 100iterations 1.9456133E-03 5.6724548E-02 at 110iterations 9.0804073E-04 2.6714325E-02 at 120iterations finished qdiffx linear iterations at : 13:59:39 total time elapsed so far: 9.650000 # loops : 120 mean,max change (kT/e) : 9.0804073E-04 2.6714325E-02 energy calculations done at 9.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.820000 DelPhi exited at 13:59:40 9.824u 0.290s 0:10.89 92.8% 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 13:59:41 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4244 !!! WARNING: HIR 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.631665 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): -25.79100 35.08300 ymin,ymax (A): 34.85500 92.30099 zmin,zma (A): 30.66900 89.29600 x,y,z range (A): 60.87400 57.44599 58.62700 scale (grids/A): 2.631665 object centre (A): 4.646000 63.57800 59.98250 number of atom coordinates read : 4244 total number of charged atoms : 4108 net assigned charge : -0.9859585 assigned positive charge : 641.3665 centred at (gu) : 95.43027 88.04642 83.97472 assigned negative charge : -642.3555 centred at (gu) : 94.72623 88.61858 84.81914 start vw surface at 0.2000000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 238016 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31647 grid for indexing accessible points = 1.400000 m= 118561 mr = 181396 m= 38742 mr = 98305 m= 8318 mr = 31430 m= 900 mr = 6454 m= 32 mr = 561 m= 0 mr = 6 time to grow re-entrant surface = 1.340000 no. cavity mid-points inaccessible to solvent = 24476 time to turn everything in is 2.240000 number of dielectric boundary points 86417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 2.400000 number of grid points assigned charge 32850 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) : 1.754444 object centre at (A) : 4.646000 63.57800 59.98250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8474642 -0.4111921 midg,1,midg; midg,igrid,midg 0.3155015 -0.3176071 1,midg,midg; igrid,midg,midg -8.5297830E-02 0.3934087 gauss-seidel spectral radius is 0.9992546 estimated iterations to convergence 289 setup time was (sec) 2.580000 now iterating at: 13:59:43 rms-change max change #iterations 11.69083 344.9976 at 10iterations 6.836903 141.2802 at 20iterations 3.971407 72.45174 at 30iterations 2.299693 43.23149 at 40iterations 1.327539 24.30298 at 50iterations 0.7662801 13.88406 at 60iterations 0.4408624 8.226830 at 70iterations 0.2538986 4.107521 at 80iterations 0.1461634 2.327407 at 90iterations 8.4177949E-02 1.333544 at 100iterations 4.8308488E-02 0.7855353 at 110iterations 2.7773337E-02 0.4559302 at 120iterations 1.5990565E-02 0.2421894 at 130iterations 9.1942688E-03 0.1443329 at 140iterations 5.3033466E-03 8.3526611E-02 at 150iterations 3.0675693E-03 5.2201271E-02 at 160iterations 1.7818762E-03 3.0139446E-02 at 170iterations 1.0466566E-03 1.7532825E-02 at 180iterations finished qdiffx linear iterations at : 13:59:58 total time elapsed so far: 16.70000 # loops : 180 mean,max change (kT/e) : 1.0466566E-03 1.7532825E-02 energy calculations done at 16.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.88000 DelPhi exited at 13:59:59 16.882u 0.290s 0:17.99 95.4% 0+0k 0+0io 0pf+0w