Tue Oct 11 06:55:49 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 06:55:49 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5487053 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): -20.37200 44.50800 ymin,ymax (A): 21.77200 78.11800 zmin,zma (A): -71.06300 -24.01900 x,y,z range (A): 64.88000 56.34600 47.04400 scale (grids/A): 0.5487053 object centre (A): 12.06800 49.94500 -47.54100 number of atom coordinates read : 2943 total number of charged atoms : 2799 net assigned charge : -1.579991 assigned positive charge : 429.6507 centred at (gu) : 89.79378 89.96739 89.78981 assigned negative charge : -431.2313 centred at (gu) : 89.79276 90.05064 89.80563 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5798 nv = 96 ne = 84 npr = 60602 no. pairs analyzed = 60602 no. exposed pairs = 3641 no. arc points = 25654 no. surface atoms = 1232 nbur = 1711 mkacc time = 0.1400000 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 = 1.568000 m= 220 mr = 3057 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3400000 number of dielectric boundary points 2940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2562 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7494 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4637668E-12 -2.1169450E-10 midg,1,midg; midg,igrid,midg 4.8256366E-10 -7.0464867E-10 1,midg,midg; igrid,midg,midg -1.2287418E-10 -9.7543959E-11 gauss-seidel spectral radius is 0.9828740 estimated iterations to convergence 63 setup time was (sec) 0.5700000 now iterating at: 06:55:50 rms-change max change #iterations 7.3213361E-02 14.40854 at 10iterations 5.1393933E-03 0.8451843 at 20iterations 4.3208274E-04 9.2809677E-02 at 30iterations 6.8762638E-05 1.7050743E-02 at 40iterations 1.6540707E-05 4.2781830E-03 at 50iterations finished qdiffx linear iterations at : 06:55:52 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.6540707E-05 4.2781830E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 06:55:53 3.363u 0.137s 0:04.16 83.8% 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 Tue Oct 11 2011 at 06:55:53 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.646116 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): -20.37200 44.50800 ymin,ymax (A): 21.77200 78.11800 zmin,zma (A): -71.06300 -24.01900 x,y,z range (A): 64.88000 56.34600 47.04400 scale (grids/A): 1.646116 object centre (A): 12.06800 49.94500 -47.54100 number of atom coordinates read : 2943 total number of charged atoms : 2799 net assigned charge : -1.579991 assigned positive charge : 429.6507 centred at (gu) : 89.38078 89.90140 89.36884 assigned negative charge : -431.2313 centred at (gu) : 89.37793 90.15163 89.41671 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 63758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25654 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20725 mr = 43415 m= 2324 mr = 14755 m= 51 mr = 1253 m= 0 mr = 4 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 27431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 239 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 21519 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) : 0.5487053 object centre at (A) : 12.06800 49.94500 -47.54100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5209768E-03 8.4274933E-03 midg,1,midg; midg,igrid,midg -3.9516827E-03 2.8487197E-03 1,midg,midg; igrid,midg,midg -2.1840839E-03 -2.2111092E-02 gauss-seidel spectral radius is 0.9982156 estimated iterations to convergence 188 setup time was (sec) 0.7600000 now iterating at: 06:55:54 rms-change max change #iterations 3.328349 141.3398 at 10iterations 1.396422 53.27656 at 20iterations 0.5846437 21.48561 at 30iterations 0.2462023 9.789292 at 40iterations 0.1037110 3.624554 at 50iterations 4.3739028E-02 1.558607 at 60iterations 1.8357055E-02 0.7031860 at 70iterations 7.7413931E-03 0.2883496 at 80iterations 3.2677066E-03 0.1134548 at 90iterations 1.3775732E-03 5.1454544E-02 at 100iterations 5.8547192E-04 2.3864746E-02 at 110iterations 2.5196283E-04 9.1524124E-03 at 120iterations finished qdiffx linear iterations at : 06:56:00 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 2.5196283E-04 9.1524124E-03 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 06:56:01 7.380u 0.164s 0:08.23 91.6% 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 06:56:01 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.469174 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): -20.37200 44.50800 ymin,ymax (A): 21.77200 78.11800 zmin,zma (A): -71.06300 -24.01900 x,y,z range (A): 64.88000 56.34600 47.04400 scale (grids/A): 2.469174 object centre (A): 12.06800 49.94500 -47.54100 number of atom coordinates read : 2943 total number of charged atoms : 2799 net assigned charge : -1.579991 assigned positive charge : 429.6507 centred at (gu) : 89.07114 89.85207 89.05318 assigned negative charge : -431.2313 centred at (gu) : 89.06662 90.22730 89.12508 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 147920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25654 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 70260 mr = 105811 m= 21249 mr = 56480 m= 3677 mr = 16576 m= 214 mr = 2536 m= 2 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.140000 number of dielectric boundary points 61832 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 22356 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) : 1.646116 object centre at (A) : 12.06800 49.94500 -47.54100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1094349 0.1408589 midg,1,midg; midg,igrid,midg -5.2287787E-02 3.7073519E-02 1,midg,midg; igrid,midg,midg -5.3487130E-02 -0.3873554 gauss-seidel spectral radius is 0.9991479 estimated iterations to convergence 271 setup time was (sec) 1.430000 now iterating at: 06:56:03 rms-change max change #iterations 8.555339 277.6111 at 10iterations 4.777100 129.5812 at 20iterations 2.658438 65.80001 at 30iterations 1.475223 33.85482 at 40iterations 0.8166674 18.22593 at 50iterations 0.4524100 10.28333 at 60iterations 0.2499070 5.474975 at 70iterations 0.1376249 2.747116 at 80iterations 7.6154515E-02 1.476223 at 90iterations 4.1942809E-02 0.8569841 at 100iterations 2.3144832E-02 0.4869804 at 110iterations 1.2753378E-02 0.2636375 at 120iterations 7.0157973E-03 0.1597176 at 130iterations 3.8663796E-03 8.2771301E-02 at 140iterations 2.1332582E-03 4.4696808E-02 at 150iterations 1.1736975E-03 2.5418758E-02 at 160iterations 6.4802024E-04 1.4076352E-02 at 170iterations 3.5646762E-04 7.3661804E-03 at 180iterations finished qdiffx linear iterations at : 06:56:13 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 3.5646762E-04 7.3661804E-03 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 06:56:14 11.632u 0.187s 0:12.34 95.7% 0+0k 0+0io 0pf+0w