Tue Oct 11 08:04:11 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 Tue Oct 11 2011 at 08:04:11 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2683 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: 0.5658967 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): 42.83300 86.32500 ymin,ymax (A): 67.47200 127.9400 zmin,zma (A): 7.551000 70.46000 x,y,z range (A): 43.49200 60.46799 62.90900 scale (grids/A): 0.5658967 object centre (A): 64.57900 97.70599 39.00550 number of atom coordinates read : 2683 total number of charged atoms : 2541 net assigned charge : 8.000012 assigned positive charge : 400.0855 centred at (gu) : 89.80239 90.84238 91.64629 assigned negative charge : -392.0865 centred at (gu) : 89.76518 90.99352 91.49648 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5544 nv = 96 ne = 84 npr = 53638 no. pairs analyzed = 53638 no. exposed pairs = 3480 no. arc points = 24315 no. surface atoms = 1179 nbur = 1504 mkacc time = 0.1200000 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= 223 mr = 2777 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2981 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2560 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7297 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1498006E-10 4.1752419E-09 midg,1,midg; midg,igrid,midg 2.3075977E-09 -1.0012311E-09 1,midg,midg; igrid,midg,midg 6.2038086E-10 1.4180163E-09 gauss-seidel spectral radius is 0.9838690 estimated iterations to convergence 65 setup time was (sec) 0.5800000 now iterating at: 08:04:12 rms-change max change #iterations 8.0911048E-02 15.69822 at 10iterations 5.9946887E-03 0.9469452 at 20iterations 4.2856278E-04 6.8691254E-02 at 30iterations 3.2132753E-05 5.3482056E-03 at 40iterations 2.3893506E-06 3.7002563E-04 at 50iterations finished qdiffx linear iterations at : 08:04:15 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 2.3893506E-06 3.7002563E-04 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 08:04:16 4.278u 0.259s 0:05.61 80.5% 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 Tue Oct 11 2011 at 08:04:16 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2683 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: 1.697690 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): 42.83300 86.32500 ymin,ymax (A): 67.47200 127.9400 zmin,zma (A): 7.551000 70.46000 x,y,z range (A): 43.49200 60.46799 62.90900 scale (grids/A): 1.697690 object centre (A): 64.57900 97.70599 39.00550 number of atom coordinates read : 2683 total number of charged atoms : 2541 net assigned charge : 8.000012 assigned positive charge : 400.0855 centred at (gu) : 89.40658 92.52695 94.93819 assigned negative charge : -392.0865 centred at (gu) : 89.29533 92.98021 94.48937 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 61060 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24315 grid for indexing accessible points = 1.400000 m= 18690 mr = 40311 m= 2149 mr = 12972 m= 65 mr = 1101 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 234 time to turn everything in is 0.4700000 number of dielectric boundary points 27573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 280 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19636 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) : 0.5658967 object centre at (A) : 64.57900 97.70599 39.00550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3201852E-03 5.1207412E-02 midg,1,midg; midg,igrid,midg 5.5601639E-03 -9.9064270E-03 1,midg,midg; igrid,midg,midg 3.2742932E-03 1.1005001E-02 gauss-seidel spectral radius is 0.9982951 estimated iterations to convergence 192 setup time was (sec) 0.8000000 now iterating at: 08:04:17 rms-change max change #iterations 3.381665 150.9579 at 10iterations 1.440645 55.36332 at 20iterations 0.6160088 20.91416 at 30iterations 0.2633425 9.211699 at 40iterations 0.1123668 4.555829 at 50iterations 4.8093356E-02 1.710997 at 60iterations 2.0590512E-02 0.9181223 at 70iterations 8.8083353E-03 0.3225756 at 80iterations 3.7774711E-03 0.1218128 at 90iterations 1.6157987E-03 6.6417694E-02 at 100iterations 6.9465168E-04 2.5887489E-02 at 110iterations 2.9743664E-04 1.0793686E-02 at 120iterations finished qdiffx linear iterations at : 08:04:26 total time elapsed so far: 9.250000 # loops : 120 mean,max change (kT/e) : 2.9743664E-04 1.0793686E-02 energy calculations done at 9.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.430000 DelPhi exited at 08:04:26 9.432u 0.275s 0:10.04 96.6% 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 Tue Oct 11 2011 at 08:04:27 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2683 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: 2.546535 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): 42.83300 86.32500 ymin,ymax (A): 67.47200 127.9400 zmin,zma (A): 7.551000 70.46000 x,y,z range (A): 43.49200 60.46799 62.90900 scale (grids/A): 2.546535 object centre (A): 64.57900 97.70599 39.00550 number of atom coordinates read : 2683 total number of charged atoms : 2541 net assigned charge : 8.000012 assigned positive charge : 400.0855 centred at (gu) : 89.10963 93.79031 97.40716 assigned negative charge : -392.0865 centred at (gu) : 88.94301 94.47021 96.73425 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 141528 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24315 grid for indexing accessible points = 1.400000 m= 64092 mr = 98491 m= 18993 mr = 50573 m= 3445 mr = 14635 m= 294 mr = 2319 m= 4 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 857 time to turn everything in is 1.150000 number of dielectric boundary points 62209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 20313 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) : 1.697690 object centre at (A) : 64.57900 97.70599 39.00550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5600369E-02 0.9420621 midg,1,midg; midg,igrid,midg 6.2578008E-02 -2.7589826E-02 1,midg,midg; igrid,midg,midg 3.8849946E-02 0.1408151 gauss-seidel spectral radius is 0.9991645 estimated iterations to convergence 273 setup time was (sec) 1.480000 now iterating at: 08:04:28 rms-change max change #iterations 8.469917 315.8435 at 10iterations 4.756708 128.8575 at 20iterations 2.668260 61.40295 at 30iterations 1.489365 33.19978 at 40iterations 0.8321751 19.29060 at 50iterations 0.4616865 10.16202 at 60iterations 0.2573618 5.738679 at 70iterations 0.1427152 3.197693 at 80iterations 7.9018138E-02 1.772581 at 90iterations 4.3878932E-02 0.9652052 at 100iterations 2.4414042E-02 0.5306988 at 110iterations 1.3499030E-02 0.2790736 at 120iterations 7.4925139E-03 0.1715126 at 130iterations 4.1471776E-03 8.4304810E-02 at 140iterations 2.2942345E-03 4.6071053E-02 at 150iterations 1.2717842E-03 2.5867462E-02 at 160iterations 7.0500368E-04 1.5417099E-02 at 170iterations 3.9025029E-04 8.4474087E-03 at 180iterations finished qdiffx linear iterations at : 08:04:42 total time elapsed so far: 14.98000 # loops : 180 mean,max change (kT/e) : 3.9025029E-04 8.4474087E-03 energy calculations done at 14.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.16000 DelPhi exited at 08:04:42 15.162u 0.272s 0:15.95 96.7% 0+0k 0+0io 0pf+0w