Tue Oct 11 03:39:44 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 Tue Oct 11 2011 at 03:39:44 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6382330 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): -11.08700 37.34200 ymin,ymax (A): -27.30000 21.50900 zmin,zma (A): -10.17000 45.60900 x,y,z range (A): 48.42900 48.80900 55.77900 scale (grids/A): 0.6382330 object centre (A): 13.12750 -2.895500 17.71950 number of atom coordinates read : 3036 total number of charged atoms : 2636 net assigned charge : 0.1620192 assigned positive charge : 420.0867 centred at (gu) : 89.86143 90.59098 91.98885 assigned negative charge : -419.9254 centred at (gu) : 89.58849 90.49713 91.90913 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7640 nv = 96 ne = 84 npr = 56559 no. pairs analyzed = 56559 no. exposed pairs = 3316 no. arc points = 23028 no. surface atoms = 1117 nbur = 1919 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 4400 m= 4 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.3100000 number of dielectric boundary points 3614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2290 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9092 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2314376E-09 1.4766959E-08 midg,1,midg; midg,igrid,midg -9.9407309E-09 1.2715648E-08 1,midg,midg; igrid,midg,midg -3.4676006E-08 3.0829387E-08 gauss-seidel spectral radius is 0.9872950 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 03:39:45 rms-change max change #iterations 0.1490517 26.46601 at 10iterations 1.4927940E-02 2.095768 at 20iterations 1.5195226E-03 0.2020187 at 30iterations 1.7490960E-04 2.8350830E-02 at 40iterations 2.6797656E-05 4.0550232E-03 at 50iterations finished qdiffx linear iterations at : 03:39:49 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 2.6797656E-05 4.0550232E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 03:39:49 4.181u 0.247s 0:04.93 89.6% 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 03:39:49 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.914699 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): -11.08700 37.34200 ymin,ymax (A): -27.30000 21.50900 zmin,zma (A): -10.17000 45.60900 x,y,z range (A): 48.42900 48.80900 55.77900 scale (grids/A): 1.914699 object centre (A): 13.12750 -2.895500 17.71950 number of atom coordinates read : 3036 total number of charged atoms : 2636 net assigned charge : 0.1620192 assigned positive charge : 420.0867 centred at (gu) : 89.58385 91.77241 95.96575 assigned negative charge : -419.9254 centred at (gu) : 88.76511 91.49106 95.72710 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82275 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23028 grid for indexing accessible points = 1.400000 m= 32102 mr = 58827 m= 5348 mr = 24557 m= 334 mr = 3442 m= 6 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 3377 time to turn everything in is 0.6200000 number of dielectric boundary points 33101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 20729 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) : 0.6382330 object centre at (A) : 13.12750 -2.895500 17.71950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3246740E-02 1.6793302E-04 midg,1,midg; midg,igrid,midg -9.1724247E-03 6.7026550E-03 1,midg,midg; igrid,midg,midg -1.5473073E-02 5.1917464E-02 gauss-seidel spectral radius is 0.9986663 estimated iterations to convergence 217 setup time was (sec) 0.9600000 now iterating at: 03:39:51 rms-change max change #iterations 4.464326 172.5193 at 10iterations 2.110574 83.71072 at 20iterations 1.000204 34.45749 at 30iterations 0.4754325 14.00594 at 40iterations 0.2246485 6.551597 at 50iterations 0.1064764 3.114654 at 60iterations 5.0487917E-02 1.549932 at 70iterations 2.3893347E-02 0.7066498 at 80iterations 1.1312689E-02 0.3577557 at 90iterations 5.3563099E-03 0.1598034 at 100iterations 2.5371315E-03 7.9488039E-02 at 110iterations 1.2034281E-03 3.6948204E-02 at 120iterations finished qdiffx linear iterations at : 03:39:59 total time elapsed so far: 9.760000 # loops : 120 mean,max change (kT/e) : 1.2034281E-03 3.6948204E-02 energy calculations done at 9.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.940000 DelPhi exited at 03:40:00 9.943u 0.269s 0:10.69 95.4% 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 03:40:00 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.872049 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): -11.08700 37.34200 ymin,ymax (A): -27.30000 21.50900 zmin,zma (A): -10.17000 45.60900 x,y,z range (A): 48.42900 48.80900 55.77900 scale (grids/A): 2.872049 object centre (A): 13.12750 -2.895500 17.71950 number of atom coordinates read : 3036 total number of charged atoms : 2636 net assigned charge : 0.1620192 assigned positive charge : 420.0867 centred at (gu) : 89.37574 92.65843 98.94836 assigned negative charge : -419.9254 centred at (gu) : 88.14765 92.23663 98.59070 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 190098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23028 grid for indexing accessible points = 1.400000 m= 102302 mr = 141947 m= 39167 mr = 85664 m= 9792 mr = 32229 m= 1456 mr = 7451 m= 84 mr = 980 m= 0 mr = 52 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 11023 time to turn everything in is 1.620000 number of dielectric boundary points 74576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 21075 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) : 1.914699 object centre at (A) : 13.12750 -2.895500 17.71950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8522481 0.2332197 midg,1,midg; midg,igrid,midg -0.1266771 5.9735039E-03 1,midg,midg; igrid,midg,midg -0.1011414 0.4754040 gauss-seidel spectral radius is 0.9992651 estimated iterations to convergence 291 setup time was (sec) 1.950000 now iterating at: 03:40:02 rms-change max change #iterations 10.40998 397.8330 at 10iterations 6.084997 142.0384 at 20iterations 3.547772 70.60182 at 30iterations 2.061503 39.45828 at 40iterations 1.195142 22.09745 at 50iterations 0.6939822 13.01569 at 60iterations 0.4015925 7.765027 at 70iterations 0.2323783 4.126320 at 80iterations 0.1341262 2.809464 at 90iterations 7.7578910E-02 1.353733 at 100iterations 4.4813380E-02 0.7813535 at 110iterations 2.5896335E-02 0.4571781 at 120iterations 1.4944215E-02 0.2771864 at 130iterations 8.6562010E-03 0.1522048 at 140iterations 5.0061475E-03 9.5275879E-02 at 150iterations 2.9094880E-03 4.8393250E-02 at 160iterations 1.6989741E-03 3.0193329E-02 at 170iterations 9.9856639E-04 1.7694473E-02 at 180iterations finished qdiffx linear iterations at : 03:40:16 total time elapsed so far: 15.70000 # loops : 180 mean,max change (kT/e) : 9.9856639E-04 1.7694473E-02 energy calculations done at 15.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.87000 DelPhi exited at 03:40:17 15.875u 0.307s 0:16.79 96.3% 0+0k 0+0io 0pf+0w