Tue Oct 11 08:34:25 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 08:34:25 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6594669 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): -15.42400 34.53200 ymin,ymax (A): 7.009000 55.27600 zmin,zma (A): 26.12100 80.10400 x,y,z range (A): 49.95600 48.26700 53.98300 scale (grids/A): 0.6594669 object centre (A): 9.554001 31.14250 53.11250 number of atom coordinates read : 2894 total number of charged atoms : 2739 net assigned charge : 1.701019 assigned positive charge : 442.2136 centred at (gu) : 89.85779 90.38931 88.91954 assigned negative charge : -440.5132 centred at (gu) : 90.11290 90.27652 88.92354 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8462 nv = 96 ne = 84 npr = 59299 no. pairs analyzed = 59299 no. exposed pairs = 3576 no. arc points = 24275 no. surface atoms = 1197 nbur = 1697 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 462 mr = 4851 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3900000 number of dielectric boundary points 4015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2418 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10032 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2659309E-09 2.6362950E-09 midg,1,midg; midg,igrid,midg -1.9431083E-08 3.1280891E-08 1,midg,midg; igrid,midg,midg 6.0916747E-08 -5.2275333E-08 gauss-seidel spectral radius is 0.9881055 estimated iterations to convergence 75 setup time was (sec) 0.6500000 now iterating at: 08:34:26 rms-change max change #iterations 0.1787466 22.61295 at 10iterations 1.9744257E-02 2.658747 at 20iterations 2.3532126E-03 0.3306274 at 30iterations 4.1617115E-04 4.7019958E-02 at 40iterations 1.2021571E-04 1.3122559E-02 at 50iterations finished qdiffx linear iterations at : 08:34:30 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.2021571E-04 1.3122559E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 08:34:30 4.177u 0.269s 0:04.75 93.2% 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 08:34:30 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! 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: 1.978401 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): -15.42400 34.53200 ymin,ymax (A): 7.009000 55.27600 zmin,zma (A): 26.12100 80.10400 x,y,z range (A): 49.95600 48.26700 53.98300 scale (grids/A): 1.978401 object centre (A): 9.554001 31.14250 53.11250 number of atom coordinates read : 2894 total number of charged atoms : 2739 net assigned charge : 1.701019 assigned positive charge : 442.2136 centred at (gu) : 89.57288 91.16749 86.75797 assigned negative charge : -440.5132 centred at (gu) : 90.33862 90.82932 86.77046 start vw surface at 0.1800000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 90603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24275 grid for indexing accessible points = 1.400000 m= 34688 mr = 64603 m= 5717 mr = 25958 m= 363 mr = 3622 m= 8 mr = 142 m= 0 mr = 2 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1300 time to turn everything in is 0.8100000 number of dielectric boundary points 37052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 21635 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) : 0.6594669 object centre at (A) : 9.554001 31.14250 53.11250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9915524E-03 -2.2131715E-02 midg,1,midg; midg,igrid,midg -1.2286943E-02 1.7527159E-02 1,midg,midg; igrid,midg,midg 8.1394330E-02 -1.1706230E-02 gauss-seidel spectral radius is 0.9987583 estimated iterations to convergence 225 setup time was (sec) 1.110000 now iterating at: 08:34:32 rms-change max change #iterations 4.935493 193.1559 at 10iterations 2.404872 76.49188 at 20iterations 1.163278 34.93683 at 30iterations 0.5671267 15.23881 at 40iterations 0.2757625 8.205913 at 50iterations 0.1339110 3.723711 at 60iterations 6.5133825E-02 1.845007 at 70iterations 3.1748462E-02 0.9627485 at 80iterations 1.5505757E-02 0.4458646 at 90iterations 7.5822528E-03 0.2304382 at 100iterations 3.7305329E-03 0.1045189 at 110iterations 1.8632644E-03 5.6979656E-02 at 120iterations finished qdiffx linear iterations at : 08:34:40 total time elapsed so far: 9.740000 # loops : 120 mean,max change (kT/e) : 1.8632644E-03 5.6979656E-02 energy calculations done at 9.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.930000 DelPhi exited at 08:34:41 9.932u 0.303s 0:10.62 96.3% 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 08:34:41 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.967601 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): -15.42400 34.53200 ymin,ymax (A): 7.009000 55.27600 zmin,zma (A): 26.12100 80.10400 x,y,z range (A): 49.95600 48.26700 53.98300 scale (grids/A): 2.967601 object centre (A): 9.554001 31.14250 53.11250 number of atom coordinates read : 2894 total number of charged atoms : 2739 net assigned charge : 1.701019 assigned positive charge : 442.2136 centred at (gu) : 89.35923 91.75122 85.13677 assigned negative charge : -440.5132 centred at (gu) : 90.50784 91.24403 85.15562 start vw surface at 0.1800000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 209498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24275 grid for indexing accessible points = 1.400000 m= 111045 mr = 155646 m= 41418 mr = 92169 m= 10279 mr = 33683 m= 1546 mr = 7701 m= 114 mr = 1019 m= 4 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 4385 time to turn everything in is 2.120000 number of dielectric boundary points 83630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 21912 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) : 1.978401 object centre at (A) : 9.554001 31.14250 53.11250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1067447 -0.3265607 midg,1,midg; midg,igrid,midg -0.1461249 0.2335319 1,midg,midg; igrid,midg,midg 0.7000765 -7.4839860E-02 gauss-seidel spectral radius is 0.9992928 estimated iterations to convergence 297 setup time was (sec) 2.480000 now iterating at: 08:34:44 rms-change max change #iterations 11.34094 414.1979 at 10iterations 6.687051 141.8465 at 20iterations 3.944803 75.75444 at 30iterations 2.318245 43.75183 at 40iterations 1.361283 26.08034 at 50iterations 0.7981808 13.78036 at 60iterations 0.4674542 8.267153 at 70iterations 0.2733316 4.414654 at 80iterations 0.1598131 2.860603 at 90iterations 9.3415119E-02 1.512537 at 100iterations 5.4506931E-02 0.9551992 at 110iterations 3.1902693E-02 0.5436020 at 120iterations 1.8623661E-02 0.3113704 at 130iterations 1.0921811E-02 0.1869659 at 140iterations 6.4281672E-03 0.1281757 at 150iterations 3.8110348E-03 6.3273430E-02 at 160iterations 2.2841471E-03 4.0138245E-02 at 170iterations 1.3973858E-03 2.6806831E-02 at 180iterations finished qdiffx linear iterations at : 08:34:58 total time elapsed so far: 16.92000 # loops : 180 mean,max change (kT/e) : 1.3973858E-03 2.6806831E-02 energy calculations done at 16.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.10000 DelPhi exited at 08:34:59 17.101u 0.310s 0:17.74 98.1% 0+0k 0+0io 0pf+0w