Mon Oct 10 14:38:08 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+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 14:38:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4282 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: 0.5679824 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): 7.704999 62.61200 ymin,ymax (A): -26.32000 34.54700 zmin,zma (A): -29.31300 33.36500 x,y,z range (A): 54.90701 60.86700 62.67800 scale (grids/A): 0.5679824 object centre (A): 35.15850 4.113501 2.026001 number of atom coordinates read : 4282 total number of charged atoms : 4159 net assigned charge : 3.500023 assigned positive charge : 639.4275 centred at (gu) : 89.97308 89.94597 89.58512 assigned negative charge : -635.9303 centred at (gu) : 90.00156 89.98354 89.66903 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 9136 nv = 96 ne = 84 npr = 86415 no. pairs analyzed = 86415 no. exposed pairs = 5536 no. arc points = 36896 no. surface atoms = 1857 nbur = 2425 mkacc time = 0.3000000 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 = 1.512000 m= 441 mr = 5002 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.6100000 number of dielectric boundary points 4549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3763 ## 389 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 11809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4692550E-09 -1.1622776E-09 midg,1,midg; midg,igrid,midg 1.2926465E-09 -2.9658470E-10 1,midg,midg; igrid,midg,midg 1.0938725E-09 -1.0768166E-10 gauss-seidel spectral radius is 0.9841073 estimated iterations to convergence 65 setup time was (sec) 0.9000000 now iterating at: 14:38:09 rms-change max change #iterations 0.1087519 13.59420 at 10iterations 9.1628330E-03 1.376102 at 20iterations 2.2179035E-03 0.2298775 at 30iterations 1.0379801E-03 0.1070404 at 40iterations 5.1581336E-04 5.4658890E-02 at 50iterations finished qdiffx linear iterations at : 14:38:13 total time elapsed so far: 4.720000 # loops : 50 mean,max change (kT/e) : 5.1581336E-04 5.4658890E-02 energy calculations done at 4.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.960000 DelPhi exited at 14:38:14 4.960u 0.426s 0:05.71 94.2% 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 Mon Oct 10 2011 at 14:38:14 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 = 4282 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: 1.703947 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): 7.704999 62.61200 ymin,ymax (A): -26.32000 34.54700 zmin,zma (A): -29.31300 33.36500 x,y,z range (A): 54.90701 60.86700 62.67800 scale (grids/A): 1.703947 object centre (A): 35.15850 4.113501 2.026001 number of atom coordinates read : 4282 total number of charged atoms : 4159 net assigned charge : 3.500023 assigned positive charge : 639.4275 centred at (gu) : 89.91792 89.83657 88.75412 assigned negative charge : -635.9303 centred at (gu) : 90.00444 89.95015 89.00638 start vw surface at 0.2100000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 100940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36896 grid for indexing accessible points = 1.400000 m= 34953 mr = 71402 m= 4472 mr = 24820 m= 163 mr = 2375 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 41906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 353 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 32196 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) : 0.5679824 object centre at (A) : 35.15850 4.113501 2.026001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5156935E-02 -1.9659666E-02 midg,1,midg; midg,igrid,midg 2.6008416E-02 9.4228750E-04 1,midg,midg; igrid,midg,midg 5.9980000E-03 6.9237924E-03 gauss-seidel spectral radius is 0.9984760 estimated iterations to convergence 203 setup time was (sec) 1.410000 now iterating at: 14:38:15 rms-change max change #iterations 4.454868 162.2828 at 10iterations 2.004504 61.34097 at 20iterations 0.8975871 27.38643 at 30iterations 0.4042576 11.16892 at 40iterations 0.1816395 4.892384 at 50iterations 8.1958503E-02 2.273746 at 60iterations 3.7187263E-02 1.003736 at 70iterations 1.7283540E-02 0.4651670 at 80iterations 8.4090615E-03 0.2462082 at 90iterations 4.5210500E-03 0.1251106 at 100iterations 2.8042914E-03 8.6383820E-02 at 110iterations 1.9724832E-03 5.0308228E-02 at 120iterations finished qdiffx linear iterations at : 14:38:28 total time elapsed so far: 13.54000 # loops : 120 mean,max change (kT/e) : 1.9724832E-03 5.0308228E-02 energy calculations done at 13.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.77000 DelPhi exited at 14:38:28 13.772u 0.482s 0:14.63 97.4% 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 14:38:28 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 = 4282 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.555921 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): 7.704999 62.61200 ymin,ymax (A): -26.32000 34.54700 zmin,zma (A): -29.31300 33.36500 x,y,z range (A): 54.90701 60.86700 62.67800 scale (grids/A): 2.555921 object centre (A): 35.15850 4.113501 2.026001 number of atom coordinates read : 4282 total number of charged atoms : 4159 net assigned charge : 3.500023 assigned positive charge : 639.4275 centred at (gu) : 89.87646 89.75447 88.13081 assigned negative charge : -635.9303 centred at (gu) : 90.00645 89.92525 88.50957 start vw surface at 0.2100000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 234303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36896 grid for indexing accessible points = 1.400000 m= 116634 mr = 174269 m= 38233 mr = 93549 m= 7381 mr = 29458 m= 682 mr = 5122 m= 13 mr = 340 m= 0 mr = 0 time to grow re-entrant surface = 1.660000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.640000 number of dielectric boundary points 94508 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 2.820000 number of grid points assigned charge 33257 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) : 1.703947 object centre at (A) : 35.15850 4.113501 2.026001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2727127 -0.3185292 midg,1,midg; midg,igrid,midg 0.4753061 -3.4641031E-02 1,midg,midg; igrid,midg,midg 0.1178254 0.1724858 gauss-seidel spectral radius is 0.9992595 estimated iterations to convergence 290 setup time was (sec) 3.030000 now iterating at: 14:38:32 rms-change max change #iterations 11.41058 287.4913 at 10iterations 6.836948 147.8724 at 20iterations 4.060243 79.83025 at 30iterations 2.390712 48.47069 at 40iterations 1.402878 23.72885 at 50iterations 0.8199528 14.71501 at 60iterations 0.4786918 8.440113 at 70iterations 0.2781394 4.800970 at 80iterations 0.1616131 3.049485 at 90iterations 9.3798429E-02 1.729770 at 100iterations 5.4446641E-02 0.9224625 at 110iterations 3.1625129E-02 0.5293112 at 120iterations 1.8483624E-02 0.3090836 at 130iterations 1.0901631E-02 0.1934061 at 140iterations 6.5618362E-03 0.1084518 at 150iterations 4.1191336E-03 6.9030762E-02 at 160iterations 2.7382253E-03 4.3563843E-02 at 170iterations 1.9665293E-03 2.8451920E-02 at 180iterations finished qdiffx linear iterations at : 14:38:49 total time elapsed so far: 19.70000 # loops : 180 mean,max change (kT/e) : 1.9665293E-03 2.8451920E-02 energy calculations done at 19.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.92000 DelPhi exited at 14:38:49 19.923u 0.532s 0:21.14 96.7% 0+0k 0+0io 0pf+0w