Mon Oct 10 10:56:04 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 10:56:04 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5416 !!! WARNING: ADP 1588 has a net charge of -2.0000 !!! WARNING: ADP 1590 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5284722 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): -20.49200 46.87200 ymin,ymax (A): -28.13000 34.99900 zmin,zma (A): -19.79900 46.11700 x,y,z range (A): 67.36400 63.12900 65.91600 scale (grids/A): 0.5284722 object centre (A): 13.19000 3.434500 13.15900 number of atom coordinates read : 5416 total number of charged atoms : 5260 net assigned charge : 6.500036 assigned positive charge : 860.6072 centred at (gu) : 91.04163 89.12717 88.83768 assigned negative charge : -854.1148 centred at (gu) : 91.01209 89.11118 88.89102 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9770 nv = 96 ne = 84 npr = 107102 no. pairs analyzed = 107102 no. exposed pairs = 6632 no. arc points = 44560 no. surface atoms = 2232 nbur = 3184 mkacc time = 0.2300000 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 = 1.624000 m= 368 mr = 5407 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.4800000 number of dielectric boundary points 4724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4481 ## 596 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 12948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2197071E-10 -1.1253399E-10 midg,1,midg; midg,igrid,midg 1.0958408E-10 2.3805125E-10 1,midg,midg; igrid,midg,midg 2.7136876E-12 4.9986093E-10 gauss-seidel spectral radius is 0.9817263 estimated iterations to convergence 61 setup time was (sec) 0.6900000 now iterating at: 10:56:05 rms-change max change #iterations 8.7886371E-02 12.61369 at 10iterations 5.9083402E-03 0.7260284 at 20iterations 8.0939004E-04 0.1520271 at 30iterations 2.7778299E-04 5.7218552E-02 at 40iterations 1.0655453E-04 2.1854401E-02 at 50iterations finished qdiffx linear iterations at : 10:56:08 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.0655453E-04 2.1854401E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 10:56:08 3.488u 0.254s 0:04.06 91.8% 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 Mon Oct 10 2011 at 10:56:08 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5416 !!! WARNING: ADP 1588 has a net charge of -2.0000 !!! WARNING: ADP 1590 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.585417 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): -20.49200 46.87200 ymin,ymax (A): -28.13000 34.99900 zmin,zma (A): -19.79900 46.11700 x,y,z range (A): 67.36400 63.12900 65.91600 scale (grids/A): 1.585417 object centre (A): 13.19000 3.434500 13.15900 number of atom coordinates read : 5416 total number of charged atoms : 5260 net assigned charge : 6.500036 assigned positive charge : 860.6072 centred at (gu) : 93.12317 87.38038 86.51130 assigned negative charge : -854.1148 centred at (gu) : 93.03644 87.33367 86.67310 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 110650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44560 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 35075 mr = 79160 m= 3206 mr = 24397 m= 76 mr = 1467 m= 0 mr = 4 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 499 time to turn everything in is 0.7400000 number of dielectric boundary points 43979 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 597 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 39945 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) : 0.5284722 object centre at (A) : 13.19000 3.434500 13.15900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9284611E-03 -3.9069135E-02 midg,1,midg; midg,igrid,midg 1.2501598E-03 -1.8300601E-04 1,midg,midg; igrid,midg,midg 2.7893975E-02 1.6249165E-02 gauss-seidel spectral radius is 0.9982978 estimated iterations to convergence 192 setup time was (sec) 1.040000 now iterating at: 10:56:09 rms-change max change #iterations 4.579708 250.8336 at 10iterations 1.964527 63.48316 at 20iterations 0.8434067 25.62299 at 30iterations 0.3618293 10.21916 at 40iterations 0.1552324 5.315170 at 50iterations 6.6790305E-02 1.925251 at 60iterations 2.8790664E-02 0.9436741 at 70iterations 1.2452238E-02 0.3633766 at 80iterations 5.4325596E-03 0.1692944 at 90iterations 2.4081299E-03 7.9883575E-02 at 100iterations 1.1161768E-03 3.6449432E-02 at 110iterations 5.5961026E-04 1.8554688E-02 at 120iterations finished qdiffx linear iterations at : 10:56:16 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 5.5961026E-04 1.8554688E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 10:56:17 7.870u 0.242s 0:08.48 95.6% 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 Mon Oct 10 2011 at 10:56:17 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5416 !!! WARNING: ADP 1588 has a net charge of -2.0000 !!! WARNING: ADP 1590 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.378125 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): -20.49200 46.87200 ymin,ymax (A): -28.13000 34.99900 zmin,zma (A): -19.79900 46.11700 x,y,z range (A): 67.36400 63.12900 65.91600 scale (grids/A): 2.378125 object centre (A): 13.19000 3.434500 13.15900 number of atom coordinates read : 5416 total number of charged atoms : 5260 net assigned charge : 6.500036 assigned positive charge : 860.6072 centred at (gu) : 94.68433 86.07024 84.76633 assigned negative charge : -854.1148 centred at (gu) : 94.55488 86.00035 85.00955 start vw surface at 0.2300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 257900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44560 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 123611 mr = 193482 m= 33173 mr = 99422 m= 4698 mr = 24561 m= 268 mr = 2869 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 1655 time to turn everything in is 1.830000 number of dielectric boundary points 99218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 42019 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) : 1.585417 object centre at (A) : 13.19000 3.434500 13.15900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8100979E-02 -1.010166 midg,1,midg; midg,igrid,midg -5.0739147E-02 -2.1207741E-02 1,midg,midg; igrid,midg,midg 0.5943489 0.2047791 gauss-seidel spectral radius is 0.9992189 estimated iterations to convergence 282 setup time was (sec) 2.130000 now iterating at: 10:56:19 rms-change max change #iterations 11.98705 335.4181 at 10iterations 7.009117 154.7435 at 20iterations 4.070010 86.82059 at 30iterations 2.346999 42.18000 at 40iterations 1.348372 27.32934 at 50iterations 0.7724189 14.31464 at 60iterations 0.4416059 7.524528 at 70iterations 0.2521582 4.483387 at 80iterations 0.1437635 2.621269 at 90iterations 8.1791639E-02 1.344299 at 100iterations 4.6512052E-02 0.8072433 at 110iterations 2.6475267E-02 0.4249986 at 120iterations 1.5056582E-02 0.2633753 at 130iterations 8.5694939E-03 0.1437988 at 140iterations 4.9057067E-03 8.6101115E-02 at 150iterations 2.8181633E-03 4.9060822E-02 at 160iterations 1.6333507E-03 3.4367561E-02 at 170iterations 9.7154576E-04 1.7967224E-02 at 180iterations finished qdiffx linear iterations at : 10:56:31 total time elapsed so far: 13.80000 # loops : 180 mean,max change (kT/e) : 9.7154576E-04 1.7967224E-02 energy calculations done at 13.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.00000 DelPhi exited at 10:56:31 13.998u 0.241s 0:14.60 97.4% 0+0k 0+0io 0pf+0w