Mon Oct 10 17:10:08 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 17:10:08 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5943140 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): -6.454000 53.44700 ymin,ymax (A): 5.272000 58.69900 zmin,zma (A): 71.33300 124.9600 x,y,z range (A): 59.90100 53.42700 53.62700 scale (grids/A): 0.5943140 object centre (A): 23.49650 31.98550 98.14650 number of atom coordinates read : 3203 total number of charged atoms : 3059 net assigned charge : 5.500041 assigned positive charge : 486.8079 centred at (gu) : 90.04248 90.09791 90.59824 assigned negative charge : -481.3093 centred at (gu) : 90.00330 90.10370 90.65019 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7398 nv = 96 ne = 84 npr = 64066 no. pairs analyzed = 64066 no. exposed pairs = 4509 no. arc points = 31941 no. surface atoms = 1484 nbur = 1719 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= 423 mr = 3512 m= 8 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2300000 number of dielectric boundary points 4277 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3152 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9344 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4274765E-09 -3.0611066E-11 midg,1,midg; midg,igrid,midg 2.1403137E-09 1.7866300E-09 1,midg,midg; igrid,midg,midg 4.7301257E-10 3.4792358E-09 gauss-seidel spectral radius is 0.9854080 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 17:10:09 rms-change max change #iterations 0.1191141 18.18335 at 10iterations 9.5155174E-03 1.494133 at 20iterations 8.2204433E-04 0.1322708 at 30iterations 7.4452553E-05 1.2699127E-02 at 40iterations 1.3425867E-05 2.2449493E-03 at 50iterations finished qdiffx linear iterations at : 17:10:12 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.3425867E-05 2.2449493E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 17:10:12 3.420u 0.165s 0:03.91 91.5% 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 Mon Oct 10 2011 at 17:10:12 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.782942 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): -6.454000 53.44700 ymin,ymax (A): 5.272000 58.69900 zmin,zma (A): 71.33300 124.9600 x,y,z range (A): 59.90100 53.42700 53.62700 scale (grids/A): 1.782942 object centre (A): 23.49650 31.98550 98.14650 number of atom coordinates read : 3203 total number of charged atoms : 3059 net assigned charge : 5.500041 assigned positive charge : 486.8079 centred at (gu) : 90.12641 90.29282 91.79420 assigned negative charge : -481.3093 centred at (gu) : 90.00991 90.31080 91.95032 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31941 grid for indexing accessible points = 1.400000 m= 26906 mr = 50230 m= 4159 mr = 17882 m= 232 mr = 2177 m= 3 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 158 time to turn everything in is 0.4000000 number of dielectric boundary points 39608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 23839 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) : 0.5943140 object centre at (A) : 23.49650 31.98550 98.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6494855E-03 -2.1783009E-03 midg,1,midg; midg,igrid,midg 1.1592447E-02 3.4162980E-03 1,midg,midg; igrid,midg,midg 4.1812258E-03 2.3887029E-02 gauss-seidel spectral radius is 0.9985280 estimated iterations to convergence 207 setup time was (sec) 0.6300000 now iterating at: 17:10:13 rms-change max change #iterations 4.217081 172.5939 at 10iterations 1.901368 72.22306 at 20iterations 0.8649875 30.52176 at 30iterations 0.3911162 14.11513 at 40iterations 0.1775827 5.825142 at 50iterations 8.0693237E-02 2.703299 at 60iterations 3.6520004E-02 1.119686 at 70iterations 1.6628176E-02 0.5150976 at 80iterations 7.5636869E-03 0.2513199 at 90iterations 3.4474276E-03 0.1017303 at 100iterations 1.5854876E-03 5.0461292E-02 at 110iterations 7.3395565E-04 2.4236679E-02 at 120iterations finished qdiffx linear iterations at : 17:10:20 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 7.3395565E-04 2.4236679E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 17:10:20 7.881u 0.183s 0:08.36 96.4% 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 17:10:21 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.674413 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): -6.454000 53.44700 ymin,ymax (A): 5.272000 58.69900 zmin,zma (A): 71.33300 124.9600 x,y,z range (A): 59.90100 53.42700 53.62700 scale (grids/A): 2.674413 object centre (A): 23.49650 31.98550 98.14650 number of atom coordinates read : 3203 total number of charged atoms : 3059 net assigned charge : 5.500041 assigned positive charge : 486.8079 centred at (gu) : 90.18947 90.43893 92.69080 assigned negative charge : -481.3093 centred at (gu) : 90.01484 90.46628 92.92539 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 181533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31941 grid for indexing accessible points = 1.400000 m= 86240 mr = 122964 m= 30686 mr = 65915 m= 7010 mr = 22924 m= 829 mr = 4610 m= 29 mr = 422 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 511 time to turn everything in is 1.000000 number of dielectric boundary points 89489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 24468 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) : 1.782942 object centre at (A) : 23.49650 31.98550 98.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7840267E-03 -2.7957151E-02 midg,1,midg; midg,igrid,midg 0.1871779 0.1067560 1,midg,midg; igrid,midg,midg 3.4349702E-02 0.2630536 gauss-seidel spectral radius is 0.9992576 estimated iterations to convergence 290 setup time was (sec) 1.250000 now iterating at: 17:10:22 rms-change max change #iterations 10.50072 289.5930 at 10iterations 6.255157 129.2012 at 20iterations 3.678652 86.46056 at 30iterations 2.153632 46.17315 at 40iterations 1.258794 25.68071 at 50iterations 0.7290906 16.62114 at 60iterations 0.4228292 8.900875 at 70iterations 0.2447194 4.936916 at 80iterations 0.1414710 2.616489 at 90iterations 8.1422590E-02 1.549584 at 100iterations 4.6792448E-02 0.8705902 at 110iterations 2.6992364E-02 0.5070496 at 120iterations 1.5509570E-02 0.2887192 at 130iterations 8.9231785E-03 0.1878031 at 140iterations 5.1396205E-03 9.0751648E-02 at 150iterations 2.9426562E-03 5.4054260E-02 at 160iterations 1.6949970E-03 3.0093193E-02 at 170iterations 9.7205862E-04 1.9078732E-02 at 180iterations finished qdiffx linear iterations at : 17:10:34 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 9.7205862E-04 1.9078732E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 17:10:34 12.986u 0.199s 0:13.46 97.8% 0+0k 0+0io 0pf+0w