Mon Oct 10 09:45:20 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 09:45:20 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 = 2900 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5706958 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): 112.3670 174.7470 ymin,ymax (A): -41.32900 10.76100 zmin,zma (A): 49.09700 103.3580 x,y,z range (A): 62.38000 52.09000 54.26100 scale (grids/A): 0.5706958 object centre (A): 143.5570 -15.28400 76.22750 number of atom coordinates read : 2900 total number of charged atoms : 2752 net assigned charge : 10.00002 assigned positive charge : 425.5159 centred at (gu) : 89.96520 88.46521 88.76903 assigned negative charge : -415.5163 centred at (gu) : 90.02476 88.52546 88.63796 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6233 nv = 96 ne = 84 npr = 56835 no. pairs analyzed = 56835 no. exposed pairs = 4441 no. arc points = 32325 no. surface atoms = 1466 nbur = 1434 mkacc time = 0.1700000 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= 305 mr = 2626 m= 3 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3157 ## 380 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8012 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9142119E-10 2.6297506E-09 midg,1,midg; midg,igrid,midg 3.5589673E-09 4.8368642E-10 1,midg,midg; igrid,midg,midg 2.4849205E-09 6.7601452E-10 gauss-seidel spectral radius is 0.9841685 estimated iterations to convergence 65 setup time was (sec) 0.6500000 now iterating at: 09:45:21 rms-change max change #iterations 8.8544875E-02 15.23540 at 10iterations 6.4494191E-03 1.110180 at 20iterations 4.8493713E-04 7.3997498E-02 at 30iterations 4.0102008E-05 6.8702698E-03 at 40iterations 4.7456642E-06 5.9795380E-04 at 50iterations finished qdiffx linear iterations at : 09:45:24 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 4.7456642E-06 5.9795380E-04 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 09:45:25 4.106u 0.254s 0:04.63 93.9% 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 Mon Oct 10 2011 at 09:45:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2900 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.712087 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): 112.3670 174.7470 ymin,ymax (A): -41.32900 10.76100 zmin,zma (A): 49.09700 103.3580 x,y,z range (A): 62.38000 52.09000 54.26100 scale (grids/A): 1.712087 object centre (A): 143.5570 -15.28400 76.22750 number of atom coordinates read : 2900 total number of charged atoms : 2752 net assigned charge : 10.00002 assigned positive charge : 425.5159 centred at (gu) : 89.89518 85.39510 86.30628 assigned negative charge : -415.5163 centred at (gu) : 90.07386 85.57606 85.91333 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 65863 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32325 grid for indexing accessible points = 1.400000 m= 20613 mr = 38767 m= 2794 mr = 13022 m= 122 mr = 1286 m= 3 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 240 time to turn everything in is 0.6300000 number of dielectric boundary points 36302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 21249 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) : 0.5706958 object centre at (A) : 143.5570 -15.28400 76.22750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9833376E-03 2.2394329E-02 midg,1,midg; midg,igrid,midg 2.1666994E-02 4.7457442E-03 1,midg,midg; igrid,midg,midg 1.4637703E-02 1.9223334E-02 gauss-seidel spectral radius is 0.9983726 estimated iterations to convergence 197 setup time was (sec) 0.9300000 now iterating at: 09:45:26 rms-change max change #iterations 3.536943 176.1812 at 10iterations 1.544407 56.29831 at 20iterations 0.6679842 22.38295 at 30iterations 0.2913976 10.67978 at 40iterations 0.1269260 4.260002 at 50iterations 5.5142891E-02 1.893326 at 60iterations 2.3964278E-02 0.9076271 at 70iterations 1.0418590E-02 0.3594663 at 80iterations 4.5491131E-03 0.1549157 at 90iterations 1.9866773E-03 7.1167231E-02 at 100iterations 8.6031517E-04 3.0920982E-02 at 110iterations 3.7719411E-04 1.5076637E-02 at 120iterations finished qdiffx linear iterations at : 09:45:34 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 3.7719411E-04 1.5076637E-02 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.410000 DelPhi exited at 09:45:35 9.411u 0.293s 0:10.20 95.0% 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 09:45:35 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 = 2900 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.568131 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): 112.3670 174.7470 ymin,ymax (A): -41.32900 10.76100 zmin,zma (A): 49.09700 103.3580 x,y,z range (A): 62.38000 52.09000 54.26100 scale (grids/A): 2.568131 object centre (A): 143.5570 -15.28400 76.22750 number of atom coordinates read : 2900 total number of charged atoms : 2752 net assigned charge : 10.00002 assigned positive charge : 425.5159 centred at (gu) : 89.84267 83.09248 84.45942 assigned negative charge : -415.5163 centred at (gu) : 90.11065 83.36401 83.86993 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 151973 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32325 grid for indexing accessible points = 1.400000 m= 67147 mr = 96037 m= 22230 mr = 49530 m= 4501 mr = 15848 m= 413 mr = 2755 m= 14 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 787 time to turn everything in is 1.510000 number of dielectric boundary points 81930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 21995 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) : 1.712087 object centre at (A) : 143.5570 -15.28400 76.22750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1044223 0.2747551 midg,1,midg; midg,igrid,midg 0.2537087 9.0081930E-02 1,midg,midg; igrid,midg,midg 0.1371553 0.2378244 gauss-seidel spectral radius is 0.9992157 estimated iterations to convergence 282 setup time was (sec) 1.830000 now iterating at: 09:45:37 rms-change max change #iterations 9.244047 292.2484 at 10iterations 5.429837 147.3308 at 20iterations 3.153919 85.19373 at 30iterations 1.820521 40.37881 at 40iterations 1.045836 24.14101 at 50iterations 0.5980700 14.86096 at 60iterations 0.3410154 7.560797 at 70iterations 0.1941067 5.332294 at 80iterations 0.1104085 2.470730 at 90iterations 6.2666178E-02 1.547698 at 100iterations 3.5601605E-02 0.7549782 at 110iterations 2.0148581E-02 0.4473495 at 120iterations 1.1400313E-02 0.2471924 at 130iterations 6.4410809E-03 0.1391006 at 140iterations 3.6446969E-03 7.6456189E-02 at 150iterations 2.0562552E-03 4.2504787E-02 at 160iterations 1.1632931E-03 2.3561478E-02 at 170iterations 6.5822573E-04 1.3088226E-02 at 180iterations finished qdiffx linear iterations at : 09:45:51 total time elapsed so far: 15.50000 # loops : 180 mean,max change (kT/e) : 6.5822573E-04 1.3088226E-02 energy calculations done at 15.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.67000 DelPhi exited at 09:45:51 15.673u 0.322s 0:16.26 98.3% 0+0k 0+0io 0pf+0w