Sat Oct 8 18:26:31 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 Sat Oct 8 2011 at 18:26:32 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 = 3240 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: 0.5873037 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): 50.24400 110.8600 ymin,ymax (A): -18.46200 41.14500 zmin,zma (A): -34.63300 24.28800 x,y,z range (A): 60.61600 59.60700 58.92101 scale (grids/A): 0.5873037 object centre (A): 80.55200 11.34150 -5.172502 number of atom coordinates read : 3240 total number of charged atoms : 3098 net assigned charge : 3.500025 assigned positive charge : 481.1587 centred at (gu) : 88.30807 89.47401 91.55399 assigned negative charge : -477.6600 centred at (gu) : 88.25196 89.63547 91.54838 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7561 nv = 96 ne = 84 npr = 64840 no. pairs analyzed = 64840 no. exposed pairs = 4299 no. arc points = 30257 no. surface atoms = 1436 nbur = 1804 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= 405 mr = 3897 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3064 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9478 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7872879E-10 1.6376756E-09 midg,1,midg; midg,igrid,midg 6.4604326E-09 -3.4683527E-09 1,midg,midg; igrid,midg,midg -1.0841292E-09 1.7961996E-09 gauss-seidel spectral radius is 0.9850642 estimated iterations to convergence 67 setup time was (sec) 0.4200000 now iterating at: 18:26:32 rms-change max change #iterations 0.1103565 17.59088 at 10iterations 9.3710134E-03 1.243382 at 20iterations 1.1290223E-03 0.1769981 at 30iterations 2.6528444E-04 4.1103363E-02 at 40iterations 7.7275239E-05 1.2008667E-02 at 50iterations finished qdiffx linear iterations at : 18:26:35 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 7.7275239E-05 1.2008667E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 18:26:36 3.448u 0.168s 0:04.05 88.8% 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 Sat Oct 8 2011 at 18:26:36 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 = 3240 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: 1.761911 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): 50.24400 110.8600 ymin,ymax (A): -18.46200 41.14500 zmin,zma (A): -34.63300 24.28800 x,y,z range (A): 60.61600 59.60700 58.92101 scale (grids/A): 1.761911 object centre (A): 80.55200 11.34150 -5.172502 number of atom coordinates read : 3240 total number of charged atoms : 3098 net assigned charge : 3.500025 assigned positive charge : 481.1587 centred at (gu) : 84.92320 88.42108 94.66114 assigned negative charge : -477.6600 centred at (gu) : 84.75542 88.90598 94.64474 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82775 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30257 grid for indexing accessible points = 1.400000 m= 28344 mr = 56005 m= 3943 mr = 19749 m= 149 mr = 2101 m= 0 mr = 24 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 62 time to turn everything in is 0.4000000 number of dielectric boundary points 37332 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 24112 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) : 0.5873037 object centre at (A) : 80.55200 11.34150 -5.172502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9844669E-03 1.8839138E-02 midg,1,midg; midg,igrid,midg 1.6737271E-02 -2.3747876E-02 1,midg,midg; igrid,midg,midg 4.6386421E-03 6.1176894E-03 gauss-seidel spectral radius is 0.9984799 estimated iterations to convergence 203 setup time was (sec) 0.6100000 now iterating at: 18:26:36 rms-change max change #iterations 4.097326 183.4128 at 10iterations 1.828675 63.03948 at 20iterations 0.8176299 27.39096 at 30iterations 0.3677392 11.22430 at 40iterations 0.1655016 5.257395 at 50iterations 7.4129596E-02 2.712739 at 60iterations 3.3379544E-02 1.063362 at 70iterations 1.5017956E-02 0.4736977 at 80iterations 6.8419795E-03 0.2153778 at 90iterations 3.1312604E-03 0.1111488 at 100iterations 1.4631500E-03 4.7157288E-02 at 110iterations 7.0548372E-04 2.4246216E-02 at 120iterations finished qdiffx linear iterations at : 18:26:44 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 7.0548372E-04 2.4246216E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 18:26:44 7.985u 0.202s 0:08.45 96.8% 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 Sat Oct 8 2011 at 18:26:44 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 = 3240 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: 2.642867 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): 50.24400 110.8600 ymin,ymax (A): -18.46200 41.14500 zmin,zma (A): -34.63300 24.28800 x,y,z range (A): 60.61600 59.60700 58.92101 scale (grids/A): 2.642867 object centre (A): 80.55200 11.34150 -5.172502 number of atom coordinates read : 3240 total number of charged atoms : 3098 net assigned charge : 3.500025 assigned positive charge : 481.1587 centred at (gu) : 82.38440 87.63142 96.99168 assigned negative charge : -477.6600 centred at (gu) : 82.13312 88.35881 96.96703 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 192034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30257 grid for indexing accessible points = 1.400000 m= 92743 mr = 136709 m= 31391 mr = 73544 m= 6480 mr = 24092 m= 641 mr = 4513 m= 26 mr = 347 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 161 time to turn everything in is 1.030000 number of dielectric boundary points 84109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 24780 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) : 1.761911 object centre at (A) : 80.55200 11.34150 -5.172502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1107777 0.1342686 midg,1,midg; midg,igrid,midg 0.2347305 -0.3150024 1,midg,midg; igrid,midg,midg 0.4420268 4.8809154E-03 gauss-seidel spectral radius is 0.9992350 estimated iterations to convergence 285 setup time was (sec) 1.270000 now iterating at: 18:26:46 rms-change max change #iterations 10.27114 362.9815 at 10iterations 6.078234 186.9316 at 20iterations 3.555174 72.61266 at 30iterations 2.066857 44.10840 at 40iterations 1.197412 25.41955 at 50iterations 0.6926555 14.26014 at 60iterations 0.3988437 7.578907 at 70iterations 0.2291235 4.598404 at 80iterations 0.1313406 2.888167 at 90iterations 7.5255267E-02 1.355693 at 100iterations 4.3070745E-02 0.8418279 at 110iterations 2.4661114E-02 0.4722595 at 120iterations 1.4092273E-02 0.2634430 at 130iterations 8.0419546E-03 0.1376343 at 140iterations 4.6067890E-03 8.9225769E-02 at 150iterations 2.6294305E-03 5.1879883E-02 at 160iterations 1.5099167E-03 2.7038574E-02 at 170iterations 8.6633553E-04 1.5628815E-02 at 180iterations finished qdiffx linear iterations at : 18:26:57 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 8.6633553E-04 1.5628815E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 18:26:58 13.184u 0.210s 0:13.74 97.4% 0+0k 0+0io 0pf+0w