Wed Dec 21 14:22:10 PST 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 Wed Dec 21 2011 at 14:22:12 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5702478 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): -35.92000 11.60600 ymin,ymax (A): -0.1480000 42.90600 zmin,zma (A): -5.482000 56.94700 x,y,z range (A): 47.52600 43.05400 62.42900 scale (grids/A): 0.5702478 object centre (A): -12.15700 21.37900 25.73250 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 90.13298 89.61578 91.18058 assigned negative charge : -287.4003 centred at (gu) : 90.01799 89.77563 91.19746 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4292 nv = 96 ne = 84 npr = 39923 no. pairs analyzed = 39923 no. exposed pairs = 2446 no. arc points = 17491 no. surface atoms = 838 nbur = 1132 mkacc time = 0.1000000 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= 206 mr = 2323 m= 0 mr = 20 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1859 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 5430 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6255007E-10 1.6980492E-10 midg,1,midg; midg,igrid,midg 2.0944779E-09 -1.2409946E-09 1,midg,midg; igrid,midg,midg -8.5999080E-10 1.5129654E-09 gauss-seidel spectral radius is 0.9840515 estimated iterations to convergence 65 setup time was (sec) 0.6000000 now iterating at: 14:22:14 rms-change max change #iterations 7.2658248E-02 14.68885 at 10iterations 5.2684122E-03 1.066021 at 20iterations 3.9578314E-04 7.6242447E-02 at 30iterations 3.0061332E-05 4.9209595E-03 at 40iterations 2.1436406E-06 4.1961670E-04 at 50iterations finished qdiffx linear iterations at : 14:22:20 total time elapsed so far: 6.360000 # loops : 50 mean,max change (kT/e) : 2.1436406E-06 4.1961670E-04 energy calculations done at 6.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.530000 DelPhi exited at 14:22:24 6.537u 0.618s 0:12.62 56.5% 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 Wed Dec 21 2011 at 14:22:26 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.710743 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): -35.92000 11.60600 ymin,ymax (A): -0.1480000 42.90600 zmin,zma (A): -5.482000 56.94700 x,y,z range (A): 47.52600 43.05400 62.42900 scale (grids/A): 1.710743 object centre (A): -12.15700 21.37900 25.73250 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 90.39886 88.84734 93.54159 assigned negative charge : -287.4003 centred at (gu) : 90.05426 89.32722 93.59274 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 46520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17491 grid for indexing accessible points = 1.400000 m= 16454 mr = 31431 m= 2051 mr = 12334 m= 60 mr = 1187 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 20116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 14252 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) : 0.5702478 object centre at (A) : -12.15700 21.37900 25.73250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5209480E-02 2.5208276E-02 midg,1,midg; midg,igrid,midg 2.1346267E-03 -8.0786264E-03 1,midg,midg; igrid,midg,midg -3.1122321E-03 7.3019136E-04 gauss-seidel spectral radius is 0.9982327 estimated iterations to convergence 189 setup time was (sec) 0.8200000 now iterating at: 14:22:28 rms-change max change #iterations 2.870095 163.4628 at 10iterations 1.208330 55.44759 at 20iterations 0.5089520 21.12389 at 30iterations 0.2142257 9.020437 at 40iterations 9.0186477E-02 3.894953 at 50iterations 3.8099367E-02 1.607229 at 60iterations 1.6022785E-02 0.6712132 at 70iterations 6.7679845E-03 0.2928123 at 80iterations 2.8658230E-03 0.1266670 at 90iterations 1.2088132E-03 5.2055359E-02 at 100iterations 5.0802401E-04 2.0502090E-02 at 110iterations 2.1471531E-04 8.6717606E-03 at 120iterations finished qdiffx linear iterations at : 14:22:37 total time elapsed so far: 9.900000 # loops : 120 mean,max change (kT/e) : 2.1471531E-04 8.6717606E-03 energy calculations done at 9.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.07000 DelPhi exited at 14:22:41 10.077u 0.725s 0:15.20 70.9% 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 Wed Dec 21 2011 at 14:22:42 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.566115 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): -35.92000 11.60600 ymin,ymax (A): -0.1480000 42.90600 zmin,zma (A): -5.482000 56.94700 x,y,z range (A): 47.52600 43.05400 62.42900 scale (grids/A): 2.566115 object centre (A): -12.15700 21.37900 25.73250 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 90.59821 88.27106 95.31239 assigned negative charge : -287.4003 centred at (gu) : 90.08147 88.99090 95.38920 start vw surface at 0.1100000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 107590 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17491 grid for indexing accessible points = 1.400000 m= 53818 mr = 76284 m= 18366 mr = 44126 m= 3427 mr = 14984 m= 290 mr = 2498 m= 9 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.5699999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 45444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 14699 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) : 1.710743 object centre at (A) : -12.15700 21.37900 25.73250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1372010 0.3250567 midg,1,midg; midg,igrid,midg -3.4093214E-04 -9.6473143E-02 1,midg,midg; igrid,midg,midg -5.9640180E-02 -1.6167555E-02 gauss-seidel spectral radius is 0.9991199 estimated iterations to convergence 266 setup time was (sec) 1.500000 now iterating at: 14:22:44 rms-change max change #iterations 7.092088 276.3061 at 10iterations 3.875117 114.2134 at 20iterations 2.119462 50.99345 at 30iterations 1.158074 26.98777 at 40iterations 0.6336798 15.68079 at 50iterations 0.3456602 8.457256 at 60iterations 0.1879521 4.744888 at 70iterations 0.1024059 2.551298 at 80iterations 5.5821478E-02 1.280083 at 90iterations 3.0374808E-02 0.7334671 at 100iterations 1.6541801E-02 0.4015274 at 110iterations 9.0330373E-03 0.2444911 at 120iterations 4.9242098E-03 0.1146526 at 130iterations 2.6760052E-03 6.4704895E-02 at 140iterations 1.4581698E-03 3.6392212E-02 at 150iterations 7.9422386E-04 1.8163681E-02 at 160iterations 4.3327731E-04 1.1140823E-02 at 170iterations 2.3593254E-04 5.3586960E-03 at 180iterations finished qdiffx linear iterations at : 14:23:05 total time elapsed so far: 22.48000 # loops : 180 mean,max change (kT/e) : 2.3593254E-04 5.3586960E-03 energy calculations done at 22.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.66000 DelPhi exited at 14:23:06 22.666u 0.646s 0:24.69 94.3% 0+0k 0+0io 0pf+0w