Tue Oct 11 06:57:44 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+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 06:57:45 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2969 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 0.5365567 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): -19.58700 46.76200 ymin,ymax (A): 21.53800 76.58000 zmin,zma (A): -72.03900 -23.56500 x,y,z range (A): 66.34900 55.04200 48.47400 scale (grids/A): 0.5365567 object centre (A): 13.58750 49.05900 -47.80200 number of atom coordinates read : 2969 total number of charged atoms : 2827 net assigned charge : -0.9609932 assigned positive charge : 434.7345 centred at (gu) : 88.82712 90.23474 89.96212 assigned negative charge : -435.6961 centred at (gu) : 88.84939 90.34311 89.97614 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5655 nv = 96 ne = 84 npr = 60236 no. pairs analyzed = 60236 no. exposed pairs = 3708 no. arc points = 26580 no. surface atoms = 1252 nbur = 1717 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 = 1.596000 m= 226 mr = 2961 m= 0 mr = 9 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2697 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7365 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2987062E-11 -1.0367904E-10 midg,1,midg; midg,igrid,midg 4.1901532E-10 -5.7375543E-10 1,midg,midg; igrid,midg,midg 8.2092957E-11 -1.0609762E-10 gauss-seidel spectral radius is 0.9821027 estimated iterations to convergence 62 setup time was (sec) 0.4000000 now iterating at: 06:57:45 rms-change max change #iterations 6.6858597E-02 10.57947 at 10iterations 4.3528182E-03 0.7216873 at 20iterations 3.0498122E-04 4.6325684E-02 at 30iterations 4.2696480E-05 1.1362076E-02 at 40iterations 1.0176467E-05 2.8858185E-03 at 50iterations finished qdiffx linear iterations at : 06:57:48 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 1.0176467E-05 2.8858185E-03 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 06:57:49 3.735u 0.178s 0:04.48 87.0% 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 06:57:49 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2969 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 1.609670 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): -19.58700 46.76200 ymin,ymax (A): 21.53800 76.58000 zmin,zma (A): -72.03900 -23.56500 x,y,z range (A): 66.34900 55.04200 48.47400 scale (grids/A): 1.609670 object centre (A): 13.58750 49.05900 -47.80200 number of atom coordinates read : 2969 total number of charged atoms : 2827 net assigned charge : -0.9609932 assigned positive charge : 434.7345 centred at (gu) : 86.48045 90.70351 89.88538 assigned negative charge : -435.6961 centred at (gu) : 86.54794 91.02882 89.92798 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26580 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20001 mr = 42401 m= 2168 mr = 14194 m= 64 mr = 1097 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 253 time to turn everything in is 0.3100000 number of dielectric boundary points 27025 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 286 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 21587 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) : 0.5365567 object centre at (A) : 13.58750 49.05900 -47.80200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2254886E-03 7.1220766E-03 midg,1,midg; midg,igrid,midg -5.3379993E-04 4.1839764E-03 1,midg,midg; igrid,midg,midg 2.0229761E-03 -2.1559348E-02 gauss-seidel spectral radius is 0.9981370 estimated iterations to convergence 184 setup time was (sec) 0.5300000 now iterating at: 06:57:50 rms-change max change #iterations 3.177002 150.2224 at 10iterations 1.301359 49.53037 at 20iterations 0.5379429 20.91852 at 30iterations 0.2216250 8.338649 at 40iterations 9.1796413E-02 3.623399 at 50iterations 3.7795976E-02 1.486128 at 60iterations 1.5576853E-02 0.5789928 at 70iterations 6.4274180E-03 0.2334113 at 80iterations 2.6484404E-03 9.6046448E-02 at 90iterations 1.0955206E-03 4.2753220E-02 at 100iterations 4.5230260E-04 1.6105652E-02 at 110iterations 1.8686405E-04 6.7138672E-03 at 120iterations finished qdiffx linear iterations at : 06:57:57 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 1.8686405E-04 6.7138672E-03 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 06:57:57 7.635u 0.198s 0:08.29 94.3% 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 06:57:57 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2969 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 2.414505 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): -19.58700 46.76200 ymin,ymax (A): 21.53800 76.58000 zmin,zma (A): -72.03900 -23.56500 x,y,z range (A): 66.34900 55.04200 48.47400 scale (grids/A): 2.414505 object centre (A): 13.58750 49.05900 -47.80200 number of atom coordinates read : 2969 total number of charged atoms : 2827 net assigned charge : -0.9609932 assigned positive charge : 434.7345 centred at (gu) : 84.72054 91.05505 89.82791 assigned negative charge : -435.6961 centred at (gu) : 84.82188 91.54314 89.89201 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 144768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26580 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 68692 mr = 103360 m= 20534 mr = 55079 m= 3380 mr = 15772 m= 218 mr = 2320 m= 4 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 883 time to turn everything in is 0.7600000 number of dielectric boundary points 60984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 22570 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) : 1.609670 object centre at (A) : 13.58750 49.05900 -47.80200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6213414E-02 0.1313782 midg,1,midg; midg,igrid,midg -1.4750172E-02 0.1342242 1,midg,midg; igrid,midg,midg -1.3902330E-02 -0.5558825 gauss-seidel spectral radius is 0.9991252 estimated iterations to convergence 267 setup time was (sec) 0.9800000 now iterating at: 06:57:59 rms-change max change #iterations 8.287214 260.5613 at 10iterations 4.594687 114.7925 at 20iterations 2.545527 62.98474 at 30iterations 1.408104 38.01096 at 40iterations 0.7775639 17.21225 at 50iterations 0.4271111 9.256172 at 60iterations 0.2345246 5.234568 at 70iterations 0.1285127 2.613797 at 80iterations 7.0609465E-02 1.813791 at 90iterations 3.8571186E-02 0.8330765 at 100iterations 2.1123456E-02 0.4887171 at 110iterations 1.1559901E-02 0.2574887 at 120iterations 6.3276631E-03 0.1542597 at 130iterations 3.4477145E-03 7.7253342E-02 at 140iterations 1.8887820E-03 3.9491653E-02 at 150iterations 1.0336124E-03 2.1102905E-02 at 160iterations 5.6446227E-04 1.2199402E-02 at 170iterations 3.0891737E-04 6.2637329E-03 at 180iterations finished qdiffx linear iterations at : 06:58:10 total time elapsed so far: 12.01000 # loops : 180 mean,max change (kT/e) : 3.0891737E-04 6.2637329E-03 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 06:58:11 12.140u 0.224s 0:13.25 93.2% 0+0k 0+0io 0pf+0w