Sun Oct 9 15:18:25 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 15:18:25 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 = 5737 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: 0.4994599 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): 67.29300 138.5700 ymin,ymax (A): -6.219000 57.05100 zmin,zma (A): -3.285000 66.32401 x,y,z range (A): 71.27699 63.27000 69.60901 scale (grids/A): 0.4994599 object centre (A): 102.9315 25.41600 31.51950 number of atom coordinates read : 5737 total number of charged atoms : 5566 net assigned charge : 1.500035 assigned positive charge : 878.5455 centred at (gu) : 89.73637 90.65427 90.08115 assigned negative charge : -877.0540 centred at (gu) : 89.79049 90.63175 90.17580 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8655 nv = 96 ne = 84 npr = 118959 no. pairs analyzed = 118959 no. exposed pairs = 6475 no. arc points = 45029 no. surface atoms = 2171 nbur = 3566 mkacc time = 0.2700000 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 = 1.708000 m= 288 mr = 4772 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.5400000 number of dielectric boundary points 4169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4316 ## 662 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 11897 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9115076E-10 -1.7934301E-10 midg,1,midg; midg,igrid,midg -2.6558039E-11 6.7333937E-11 1,midg,midg; igrid,midg,midg 1.2640043E-10 -8.7809218E-11 gauss-seidel spectral radius is 0.9795558 estimated iterations to convergence 58 setup time was (sec) 0.7700000 now iterating at: 15:18:26 rms-change max change #iterations 6.7356892E-02 10.28160 at 10iterations 4.6249405E-03 0.6653099 at 20iterations 7.8136084E-04 9.0765953E-02 at 30iterations 2.0818801E-04 2.5089264E-02 at 40iterations 6.1333383E-05 7.3242188E-03 at 50iterations finished qdiffx linear iterations at : 15:18:28 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 6.1333383E-05 7.3242188E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 15:18:29 3.587u 0.157s 0:04.03 92.5% 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 15:18:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5737 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: 1.498380 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): 67.29300 138.5700 ymin,ymax (A): -6.219000 57.05100 zmin,zma (A): -3.285000 66.32401 x,y,z range (A): 71.27699 63.27000 69.60901 scale (grids/A): 1.498380 object centre (A): 102.9315 25.41600 31.51950 number of atom coordinates read : 5737 total number of charged atoms : 5566 net assigned charge : 1.500035 assigned positive charge : 878.5455 centred at (gu) : 89.20710 91.96097 90.24144 assigned negative charge : -877.0540 centred at (gu) : 89.37123 91.89520 90.52724 start vw surface at 0.2300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 100198 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45029 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 28039 mr = 71265 m= 2291 mr = 19136 m= 54 mr = 1016 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 4643 time to turn everything in is 0.7200000 number of dielectric boundary points 39165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 657 ## 14 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 41556 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) : 0.4994599 object centre at (A) : 102.9315 25.41600 31.51950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1593512E-03 3.4769170E-03 midg,1,midg; midg,igrid,midg -1.3265036E-03 5.3861416E-03 1,midg,midg; igrid,midg,midg -1.4840051E-02 -5.3409520E-03 gauss-seidel spectral radius is 0.9980873 estimated iterations to convergence 182 setup time was (sec) 1.010000 now iterating at: 15:18:30 rms-change max change #iterations 4.065655 154.1089 at 10iterations 1.653059 54.82905 at 20iterations 0.6759132 19.63574 at 30iterations 0.2759992 8.604393 at 40iterations 0.1128071 3.434288 at 50iterations 4.6208151E-02 1.550774 at 60iterations 1.9031869E-02 0.5470926 at 70iterations 7.8516435E-03 0.2367897 at 80iterations 3.2700943E-03 0.1065941 at 90iterations 1.3999045E-03 4.8079014E-02 at 100iterations 6.3163968E-04 1.8133834E-02 at 110iterations 3.0882587E-04 8.8806152E-03 at 120iterations finished qdiffx linear iterations at : 15:18:37 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 3.0882587E-04 8.8806152E-03 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 15:18:37 7.944u 0.180s 0:08.46 95.9% 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 15:18:38 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 = 5737 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: 2.247570 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): 67.29300 138.5700 ymin,ymax (A): -6.219000 57.05100 zmin,zma (A): -3.285000 66.32401 x,y,z range (A): 71.27699 63.27000 69.60901 scale (grids/A): 2.247570 object centre (A): 102.9315 25.41600 31.51950 number of atom coordinates read : 5737 total number of charged atoms : 5566 net assigned charge : 1.500035 assigned positive charge : 878.5455 centred at (gu) : 88.81033 92.94083 90.36175 assigned negative charge : -877.0540 centred at (gu) : 89.05676 92.84290 90.79064 start vw surface at 0.2400000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 234476 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45029 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 103007 mr = 175200 m= 25127 mr = 81912 m= 3172 mr = 18450 m= 122 mr = 1891 m= 0 mr = 41 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 15273 time to turn everything in is 1.730000 number of dielectric boundary points 88410 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 44374 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) : 1.498380 object centre at (A) : 102.9315 25.41600 31.51950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4856747E-02 0.2002572 midg,1,midg; midg,igrid,midg -5.3339344E-02 0.1637165 1,midg,midg; igrid,midg,midg -0.5142846 0.2037023 gauss-seidel spectral radius is 0.9991661 estimated iterations to convergence 273 setup time was (sec) 2.040000 now iterating at: 15:18:40 rms-change max change #iterations 11.00933 304.3386 at 10iterations 6.267284 129.8737 at 20iterations 3.553128 83.48152 at 30iterations 2.003529 38.86083 at 40iterations 1.127069 26.16997 at 50iterations 0.6318785 11.94007 at 60iterations 0.3539199 6.236544 at 70iterations 0.1977995 3.593235 at 80iterations 0.1103441 2.055462 at 90iterations 6.1677616E-02 1.097412 at 100iterations 3.4424134E-02 0.7517090 at 110iterations 1.9182265E-02 0.3639221 at 120iterations 1.0684161E-02 0.1849022 at 130iterations 5.9516728E-03 0.1048965 at 140iterations 3.3280957E-03 6.5379143E-02 at 150iterations 1.8560578E-03 3.3981323E-02 at 160iterations 1.0429294E-03 1.7398834E-02 at 170iterations 5.8808608E-04 1.0372162E-02 at 180iterations finished qdiffx linear iterations at : 15:18:51 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 5.8808608E-04 1.0372162E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 15:18:51 13.077u 0.183s 0:13.54 97.8% 0+0k 0+0io 0pf+0w