Sun Oct 9 04:07:25 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 Sun Oct 9 2011 at 04:07:25 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4546 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.3425382 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): -9.763000 85.17500 ymin,ymax (A): -47.19000 11.55100 zmin,zma (A): -92.47500 11.45500 x,y,z range (A): 94.93800 58.74100 103.9300 scale (grids/A): 0.3425382 object centre (A): 37.70600 -17.81950 -40.51000 number of atom coordinates read : 4546 total number of charged atoms : 4232 net assigned charge : 22.80000 assigned positive charge : 662.8417 centred at (gu) : 84.77554 88.80860 82.87637 assigned negative charge : -640.0459 centred at (gu) : 84.64744 88.80402 82.74023 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 3066 nv = 96 ne = 84 npr = 87591 no. pairs analyzed = 87591 no. exposed pairs = 6396 no. arc points = 45047 no. surface atoms = 2116 nbur = 2430 mkacc time = 0.2000000 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 = 2.436000 m= 60 mr = 1201 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 1925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2512 ## 727 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 4117 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5983827E-14 7.9627280E-16 midg,1,midg; midg,igrid,midg 7.5542405E-15 3.3402537E-15 1,midg,midg; igrid,midg,midg -7.9783727E-15 1.5182842E-15 gauss-seidel spectral radius is 0.9570108 estimated iterations to convergence 41 setup time was (sec) 0.6800000 now iterating at: 04:07:26 rms-change max change #iterations 9.2659211E-03 2.327480 at 10iterations 1.1784225E-03 0.3237610 at 20iterations 2.0990609E-04 5.0785065E-02 at 30iterations 3.7914691E-05 8.4953308E-03 at 40iterations 6.8700783E-06 1.5430450E-03 at 50iterations finished qdiffx linear iterations at : 04:07:29 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 6.8700783E-06 1.5430450E-03 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 04:07:30 4.399u 0.241s 0:04.95 93.5% 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 Sun Oct 9 2011 at 04:07:30 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4546 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.027615 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): -9.763000 85.17500 ymin,ymax (A): -47.19000 11.55100 zmin,zma (A): -92.47500 11.45500 x,y,z range (A): 94.93800 58.74100 103.9300 scale (grids/A): 1.027615 object centre (A): 37.70600 -17.81950 -40.51000 number of atom coordinates read : 4546 total number of charged atoms : 4232 net assigned charge : 22.80000 assigned positive charge : 662.8417 centred at (gu) : 74.32513 86.42455 68.62763 assigned negative charge : -640.0459 centred at (gu) : 73.94199 86.41160 68.22034 start vw surface at 0.2200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 37827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45047 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.268000 m= 6221 mr = 22725 m= 147 mr = 2950 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 50 time to turn everything in is 0.4800000 number of dielectric boundary points 18516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1297 ## 82 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 25381 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) : 0.3425382 object centre at (A) : 37.70600 -17.81950 -40.51000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6768406E-03 1.1694334E-03 midg,1,midg; midg,igrid,midg 1.9831271E-04 1.1673624E-04 1,midg,midg; igrid,midg,midg 1.0508660E-03 2.2810964E-04 gauss-seidel spectral radius is 0.9952778 estimated iterations to convergence 117 setup time was (sec) 0.8200000 now iterating at: 04:07:31 rms-change max change #iterations 1.187503 77.73603 at 10iterations 0.2894778 18.72581 at 20iterations 7.1488000E-02 4.029334 at 30iterations 1.8185718E-02 1.025063 at 40iterations 5.2177440E-03 0.2881317 at 50iterations 1.9737573E-03 0.1112118 at 60iterations 9.6834567E-04 4.7065735E-02 at 70iterations 5.3063582E-04 2.4921417E-02 at 80iterations 2.9761664E-04 1.4089584E-02 at 90iterations 1.6830109E-04 8.0442429E-03 at 100iterations 9.5428368E-05 4.5862198E-03 at 110iterations 5.4166787E-05 2.6178360E-03 at 120iterations finished qdiffx linear iterations at : 04:07:39 total time elapsed so far: 9.130000 # loops : 120 mean,max change (kT/e) : 5.4166787E-05 2.6178360E-03 energy calculations done at 9.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.290000 DelPhi exited at 04:07:40 9.296u 0.255s 0:09.84 96.9% 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 Sun Oct 9 2011 at 04:07:40 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4546 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.541422 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): -9.763000 85.17500 ymin,ymax (A): -47.19000 11.55100 zmin,zma (A): -92.47500 11.45500 x,y,z range (A): 94.93800 58.74100 103.9300 scale (grids/A): 1.541422 object centre (A): 37.70600 -17.81950 -40.51000 number of atom coordinates read : 4546 total number of charged atoms : 4232 net assigned charge : 22.80000 assigned positive charge : 662.8417 centred at (gu) : 66.48752 84.63651 57.94119 assigned negative charge : -640.0459 centred at (gu) : 65.91292 84.61746 57.33036 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 89217 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45047 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.240000 m= 27380 mr = 58141 m= 2624 mr = 18185 m= 62 mr = 1134 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 201 time to turn everything in is 0.8000000 number of dielectric boundary points 41823 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 543 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 31889 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) : 1.027615 object centre at (A) : 37.70600 -17.81950 -40.51000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1674566 4.5513034E-02 midg,1,midg; midg,igrid,midg 8.1901588E-03 4.4911010E-03 1,midg,midg; igrid,midg,midg 6.6223428E-02 4.8532267E-03 gauss-seidel spectral radius is 0.9979481 estimated iterations to convergence 176 setup time was (sec) 1.140000 now iterating at: 04:07:41 rms-change max change #iterations 4.305422 209.7999 at 10iterations 1.790877 80.50548 at 20iterations 0.7325428 34.53512 at 30iterations 0.2990230 13.28828 at 40iterations 0.1210886 5.123928 at 50iterations 4.8913099E-02 1.999714 at 60iterations 1.9718781E-02 0.7506731 at 70iterations 8.0018770E-03 0.2878475 at 80iterations 3.3333213E-03 0.1186483 at 90iterations 1.4594794E-03 4.8938751E-02 at 100iterations 7.0976181E-04 2.2805214E-02 at 110iterations 3.9299310E-04 1.3687134E-02 at 120iterations 2.4132285E-04 6.5326691E-03 at 130iterations 1.5719105E-04 4.2247772E-03 at 140iterations 1.0512112E-04 2.7313232E-03 at 150iterations 7.1108952E-05 1.8548965E-03 at 160iterations 4.8362373E-05 1.2683868E-03 at 170iterations 3.2972373E-05 8.7165833E-04 at 180iterations finished qdiffx linear iterations at : 04:07:54 total time elapsed so far: 13.98000 # loops : 180 mean,max change (kT/e) : 3.2972373E-05 8.7165833E-04 energy calculations done at 13.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.16000 DelPhi exited at 04:07:54 14.162u 0.261s 0:14.69 98.1% 0+0k 0+0io 0pf+0w