Tue Oct 11 06:01:21 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 06:01:21 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7041557 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): 25.57000 72.41200 ymin,ymax (A): -18.93400 31.62300 zmin,zma (A): 3.881000 46.31400 x,y,z range (A): 46.84200 50.55700 42.43300 scale (grids/A): 0.7041557 object centre (A): 48.99100 6.344501 25.09750 number of atom coordinates read : 2327 total number of charged atoms : 1998 net assigned charge : 5.564011 assigned positive charge : 326.4259 centred at (gu) : 89.19177 90.21844 90.39239 assigned negative charge : -320.8621 centred at (gu) : 89.30653 90.15399 90.48275 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7167 nv = 96 ne = 84 npr = 42269 no. pairs analyzed = 42269 no. exposed pairs = 2616 no. arc points = 17848 no. surface atoms = 904 nbur = 1423 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 482 mr = 4107 m= 3 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1642 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8031 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.9123055E-08 -2.0407605E-10 midg,1,midg; midg,igrid,midg 1.2021350E-08 7.6504428E-08 1,midg,midg; igrid,midg,midg 1.1328238E-07 -9.6382538E-09 gauss-seidel spectral radius is 0.9894920 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 06:01:22 rms-change max change #iterations 0.2001406 25.71670 at 10iterations 2.5281785E-02 3.222097 at 20iterations 3.7415510E-03 0.5133753 at 30iterations 8.0151402E-04 9.5731258E-02 at 40iterations 2.4358426E-04 2.7294159E-02 at 50iterations finished qdiffx linear iterations at : 06:01:25 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 2.4358426E-04 2.7294159E-02 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.380000 DelPhi exited at 06:01:26 4.388u 0.395s 0:05.09 93.7% 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 06:01:26 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.112467 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): 25.57000 72.41200 ymin,ymax (A): -18.93400 31.62300 zmin,zma (A): 3.881000 46.31400 x,y,z range (A): 46.84200 50.55700 42.43300 scale (grids/A): 2.112467 object centre (A): 48.99100 6.344501 25.09750 number of atom coordinates read : 2327 total number of charged atoms : 1998 net assigned charge : 5.564011 assigned positive charge : 326.4259 centred at (gu) : 87.57518 90.65520 91.17700 assigned negative charge : -320.8621 centred at (gu) : 87.91942 90.46208 91.44810 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76120 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17848 grid for indexing accessible points = 1.400000 m= 31195 mr = 54239 m= 5934 mr = 23855 m= 541 mr = 3914 m= 21 mr = 244 m= 0 mr = 2 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 31557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 15847 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) : 0.7041557 object centre at (A) : 48.99100 6.344501 25.09750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2595778E-02 2.1871204E-02 midg,1,midg; midg,igrid,midg 3.6829345E-02 2.3383880E-02 1,midg,midg; igrid,midg,midg 4.0549032E-02 -4.1457519E-02 gauss-seidel spectral radius is 0.9988266 estimated iterations to convergence 231 setup time was (sec) 0.9900000 now iterating at: 06:01:27 rms-change max change #iterations 4.665779 178.6817 at 10iterations 2.298769 85.14046 at 20iterations 1.139721 34.60166 at 30iterations 0.5648533 16.81523 at 40iterations 0.2806922 8.536518 at 50iterations 0.1394054 4.365311 at 60iterations 6.9074817E-02 1.982891 at 70iterations 3.4475930E-02 1.125404 at 80iterations 1.7353879E-02 0.5682831 at 90iterations 8.7345475E-03 0.2740645 at 100iterations 4.4799666E-03 0.1386585 at 110iterations 2.3807622E-03 7.0213318E-02 at 120iterations finished qdiffx linear iterations at : 06:01:37 total time elapsed so far: 10.47000 # loops : 120 mean,max change (kT/e) : 2.3807622E-03 7.0213318E-02 energy calculations done at 10.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.63000 DelPhi exited at 06:01:38 10.636u 0.454s 0:11.56 95.8% 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 Tue Oct 11 2011 at 06:01:38 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.168701 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): 25.57000 72.41200 ymin,ymax (A): -18.93400 31.62300 zmin,zma (A): 3.881000 46.31400 x,y,z range (A): 46.84200 50.55700 42.43300 scale (grids/A): 3.168701 object centre (A): 48.99100 6.344501 25.09750 number of atom coordinates read : 2327 total number of charged atoms : 1998 net assigned charge : 5.564011 assigned positive charge : 326.4259 centred at (gu) : 86.36274 90.98289 91.76546 assigned negative charge : -320.8621 centred at (gu) : 86.87914 90.69315 92.17215 start vw surface at 0.1200000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 175191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17848 grid for indexing accessible points = 1.400000 m= 96598 mr = 130173 m= 39738 mr = 80822 m= 11241 mr = 32775 m= 2169 mr = 8649 m= 263 mr = 1545 m= 12 mr = 167 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.020000 number of dielectric boundary points 71081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 15984 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) : 2.112467 object centre at (A) : 48.99100 6.344501 25.09750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1444163 0.1849457 midg,1,midg; midg,igrid,midg 0.2851541 8.8659443E-02 1,midg,midg; igrid,midg,midg 0.4095103 -0.5097641 gauss-seidel spectral radius is 0.9992972 estimated iterations to convergence 298 setup time was (sec) 2.360000 now iterating at: 06:01:40 rms-change max change #iterations 10.45003 436.8414 at 10iterations 6.197668 130.0800 at 20iterations 3.668868 79.26579 at 30iterations 2.162493 38.76373 at 40iterations 1.276184 25.21436 at 50iterations 0.7516171 15.90001 at 60iterations 0.4414481 8.243948 at 70iterations 0.2584096 4.815718 at 80iterations 0.1520127 2.721216 at 90iterations 8.9135751E-02 1.790276 at 100iterations 5.2478004E-02 0.9814963 at 110iterations 3.0897042E-02 0.5765381 at 120iterations 1.8406773E-02 0.3468246 at 130iterations 1.1149570E-02 0.2076569 at 140iterations 6.9012437E-03 0.1272430 at 150iterations 4.4346391E-03 9.5211029E-02 at 160iterations 3.0143808E-03 5.8742523E-02 at 170iterations 2.1730142E-03 4.0596008E-02 at 180iterations finished qdiffx linear iterations at : 06:01:56 total time elapsed so far: 18.38000 # loops : 180 mean,max change (kT/e) : 2.1730142E-03 4.0596008E-02 energy calculations done at 18.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.54000 DelPhi exited at 06:01:58 18.547u 0.462s 0:19.94 95.2% 0+0k 0+0io 0pf+0w