Mon Oct 10 18:30:28 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 18:30:28 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 = 2515 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5929874 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): 10.71700 65.86200 ymin,ymax (A): -42.22400 15.03600 zmin,zma (A): -20.39300 39.64200 x,y,z range (A): 55.14500 57.26000 60.03500 scale (grids/A): 0.5929874 object centre (A): 38.28950 -13.59400 9.624501 number of atom coordinates read : 2515 total number of charged atoms : 2376 net assigned charge : 13.50000 assigned positive charge : 373.9417 centred at (gu) : 89.05930 89.76725 90.93941 assigned negative charge : -360.4426 centred at (gu) : 89.05318 89.69821 90.89547 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6009 nv = 96 ne = 84 npr = 49906 no. pairs analyzed = 49906 no. exposed pairs = 3356 no. arc points = 24050 no. surface atoms = 1117 nbur = 1398 mkacc time = 0.1100000 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 = 1.456000 m= 280 mr = 3023 m= 3 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2700000 number of dielectric boundary points 3256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2440 ## 275 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7395 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7562945E-09 7.1269204E-09 midg,1,midg; midg,igrid,midg 2.8247100E-09 6.1096794E-09 1,midg,midg; igrid,midg,midg 5.4400529E-09 3.8531041E-09 gauss-seidel spectral radius is 0.9852840 estimated iterations to convergence 68 setup time was (sec) 0.4900000 now iterating at: 18:30:28 rms-change max change #iterations 9.7807802E-02 15.79126 at 10iterations 7.9128742E-03 1.189133 at 20iterations 6.7895092E-04 0.1153545 at 30iterations 6.3345666E-05 9.7303391E-03 at 40iterations 7.5270127E-06 1.1518002E-03 at 50iterations finished qdiffx linear iterations at : 18:30:31 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 7.5270127E-06 1.1518002E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 18:30:31 3.086u 0.127s 0:03.53 90.6% 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 18:30:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2515 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.778962 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): 10.71700 65.86200 ymin,ymax (A): -42.22400 15.03600 zmin,zma (A): -20.39300 39.64200 x,y,z range (A): 55.14500 57.26000 60.03500 scale (grids/A): 1.778962 object centre (A): 38.28950 -13.59400 9.624501 number of atom coordinates read : 2515 total number of charged atoms : 2376 net assigned charge : 13.50000 assigned positive charge : 373.9417 centred at (gu) : 87.17725 89.30138 92.81757 assigned negative charge : -360.4426 centred at (gu) : 87.15916 89.09434 92.68637 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 64917 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24050 grid for indexing accessible points = 1.400000 m= 21430 mr = 43115 m= 2705 mr = 14856 m= 100 mr = 1413 m= 0 mr = 12 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1537 time to turn everything in is 0.4500000 number of dielectric boundary points 29756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 239 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 18511 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) : 0.5929874 object centre at (A) : 38.28950 -13.59400 9.624501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3824019E-02 5.1168341E-02 midg,1,midg; midg,igrid,midg 1.1698497E-02 2.2708351E-02 1,midg,midg; igrid,midg,midg 1.0678377E-02 3.3952482E-03 gauss-seidel spectral radius is 0.9984362 estimated iterations to convergence 201 setup time was (sec) 0.7000000 now iterating at: 18:30:32 rms-change max change #iterations 3.531882 182.9577 at 10iterations 1.556611 59.65408 at 20iterations 0.6898657 24.30815 at 30iterations 0.3047876 10.47793 at 40iterations 0.1353962 4.591286 at 50iterations 5.9719443E-02 2.186363 at 60iterations 2.6541123E-02 0.9708462 at 70iterations 1.1767076E-02 0.4489307 at 80iterations 5.2086692E-03 0.1874542 at 90iterations 2.3190095E-03 8.8276863E-02 at 100iterations 1.0324273E-03 3.9730072E-02 at 110iterations 4.5813367E-04 1.7944336E-02 at 120iterations finished qdiffx linear iterations at : 18:30:38 total time elapsed so far: 6.630000 # loops : 120 mean,max change (kT/e) : 4.5813367E-04 1.7944336E-02 energy calculations done at 6.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.800000 DelPhi exited at 18:30:39 6.805u 0.182s 0:07.40 94.3% 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 18:30:39 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 = 2515 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.668443 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): 10.71700 65.86200 ymin,ymax (A): -42.22400 15.03600 zmin,zma (A): -20.39300 39.64200 x,y,z range (A): 55.14500 57.26000 60.03500 scale (grids/A): 2.668443 object centre (A): 38.28950 -13.59400 9.624501 number of atom coordinates read : 2515 total number of charged atoms : 2376 net assigned charge : 13.50000 assigned positive charge : 373.9417 centred at (gu) : 85.76567 88.95193 94.22626 assigned negative charge : -360.4426 centred at (gu) : 85.73871 88.64154 94.02939 start vw surface at 0.1300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 150258 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24050 grid for indexing accessible points = 1.400000 m= 71891 mr = 105353 m= 22854 mr = 56825 m= 4523 mr = 17297 m= 416 mr = 3105 m= 12 mr = 211 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 5360 time to turn everything in is 1.100000 number of dielectric boundary points 67163 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 18996 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) : 1.778962 object centre at (A) : 38.28950 -13.59400 9.624501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4072399 0.8216029 midg,1,midg; midg,igrid,midg 9.4952285E-02 0.2592757 1,midg,midg; igrid,midg,midg 7.3014632E-02 3.7376184E-03 gauss-seidel spectral radius is 0.9992061 estimated iterations to convergence 280 setup time was (sec) 1.360000 now iterating at: 18:30:40 rms-change max change #iterations 8.807950 442.0191 at 10iterations 5.115673 124.9875 at 20iterations 2.937581 64.07391 at 30iterations 1.677266 37.06150 at 40iterations 0.9536817 22.95865 at 50iterations 0.5408735 12.72370 at 60iterations 0.3059680 7.192996 at 70iterations 0.1728897 3.366179 at 80iterations 9.7881354E-02 2.227146 at 90iterations 5.5092655E-02 1.092987 at 100iterations 3.1088378E-02 0.6391836 at 110iterations 1.7513687E-02 0.3760185 at 120iterations 9.8711886E-03 0.2016516 at 130iterations 5.5755065E-03 0.1202812 at 140iterations 3.1418796E-03 6.4668655E-02 at 150iterations 1.7630502E-03 3.3027649E-02 at 160iterations 9.9276681E-04 2.0647049E-02 at 170iterations 5.6244293E-04 1.1464119E-02 at 180iterations finished qdiffx linear iterations at : 18:30:50 total time elapsed so far: 11.36000 # loops : 180 mean,max change (kT/e) : 5.6244293E-04 1.1464119E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.54000 DelPhi exited at 18:30:51 11.547u 0.194s 0:12.05 97.3% 0+0k 0+0io 0pf+0w