Sat Oct 15 15:17:15 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 Sat Oct 15 2011 at 15:17:15 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2685 !!! WARNING: ASP 40 has a net charge of -2.0000 !!! WARNING: HIR 83 has a net charge of 0.5140 !!! WARNING: SEP 231 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6435286 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): -7.014000 48.30600 ymin,ymax (A): 16.72400 70.07300 zmin,zma (A): -7.764000 39.37900 x,y,z range (A): 55.32000 53.34900 47.14300 scale (grids/A): 0.6435286 object centre (A): 20.64600 43.39850 15.80750 number of atom coordinates read : 2685 total number of charged atoms : 2538 net assigned charge : 5.039020 assigned positive charge : 405.9800 centred at (gu) : 90.68425 89.96286 89.42263 assigned negative charge : -400.9415 centred at (gu) : 90.98242 90.10180 89.66270 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7401 nv = 96 ne = 84 npr = 54642 no. pairs analyzed = 54642 no. exposed pairs = 3417 no. arc points = 23532 no. surface atoms = 1127 nbur = 1558 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 438 mr = 4102 m= 4 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2374 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8965 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4528008E-08 -2.1421993E-08 midg,1,midg; midg,igrid,midg 2.6670701E-08 -1.0283103E-08 1,midg,midg; igrid,midg,midg 4.0240892E-08 -3.7823938E-08 gauss-seidel spectral radius is 0.9874957 estimated iterations to convergence 73 setup time was (sec) 0.5200000 now iterating at: 15:17:15 rms-change max change #iterations 0.1548871 21.85637 at 10iterations 1.5947936E-02 2.095448 at 20iterations 1.7723992E-03 0.2481594 at 30iterations 2.8111230E-04 3.7272453E-02 at 40iterations 8.1605198E-05 1.2079239E-02 at 50iterations finished qdiffx linear iterations at : 15:17:18 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 8.1605198E-05 1.2079239E-02 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 15:17:18 3.144u 0.153s 0:03.56 92.4% 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 Sat Oct 15 2011 at 15:17:18 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2685 !!! WARNING: ASP 40 has a net charge of -2.0000 !!! WARNING: HIR 83 has a net charge of 0.5140 !!! WARNING: SEP 231 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.930586 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): -7.014000 48.30600 ymin,ymax (A): 16.72400 70.07300 zmin,zma (A): -7.764000 39.37900 x,y,z range (A): 55.32000 53.34900 47.14300 scale (grids/A): 1.930586 object centre (A): 20.64600 43.39850 15.80750 number of atom coordinates read : 2685 total number of charged atoms : 2538 net assigned charge : 5.039020 assigned positive charge : 405.9800 centred at (gu) : 92.05231 89.88811 88.26756 assigned negative charge : -400.9415 centred at (gu) : 92.94711 90.30499 88.98795 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23532 grid for indexing accessible points = 1.400000 m= 28909 mr = 55065 m= 4675 mr = 21230 m= 284 mr = 2980 m= 3 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 901 time to turn everything in is 0.5500000 number of dielectric boundary points 34055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19981 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) : 0.6435286 object centre at (A) : 20.64600 43.39850 15.80750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8225816E-02 -1.2867983E-02 midg,1,midg; midg,igrid,midg 2.9437698E-02 -2.4487441E-03 1,midg,midg; igrid,midg,midg 9.7734563E-02 -6.5566063E-02 gauss-seidel spectral radius is 0.9986816 estimated iterations to convergence 218 setup time was (sec) 0.8200000 now iterating at: 15:17:19 rms-change max change #iterations 4.476528 181.1786 at 10iterations 2.123610 85.58536 at 20iterations 1.007254 31.49092 at 30iterations 0.4773319 15.06732 at 40iterations 0.2274988 7.228475 at 50iterations 0.1077741 3.527092 at 60iterations 5.1227916E-02 1.673813 at 70iterations 2.4309827E-02 0.7971153 at 80iterations 1.1636007E-02 0.3519440 at 90iterations 5.5545596E-03 0.1906548 at 100iterations 2.6746462E-03 8.3774567E-02 at 110iterations 1.3034332E-03 4.1763306E-02 at 120iterations finished qdiffx linear iterations at : 15:17:32 total time elapsed so far: 6.950000 # loops : 120 mean,max change (kT/e) : 1.3034332E-03 4.1763306E-02 energy calculations done at 6.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.130000 DelPhi exited at 15:17:33 7.129u 0.165s 0:15.04 48.4% 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 Sat Oct 15 2011 at 15:17:34 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2685 !!! WARNING: ASP 40 has a net charge of -2.0000 !!! WARNING: HIR 83 has a net charge of 0.5140 !!! WARNING: SEP 231 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.895879 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): -7.014000 48.30600 ymin,ymax (A): 16.72400 70.07300 zmin,zma (A): -7.764000 39.37900 x,y,z range (A): 55.32000 53.34900 47.14300 scale (grids/A): 2.895879 object centre (A): 20.64600 43.39850 15.80750 number of atom coordinates read : 2685 total number of charged atoms : 2538 net assigned charge : 5.039020 assigned positive charge : 405.9800 centred at (gu) : 93.07854 89.83192 87.40126 assigned negative charge : -400.9415 centred at (gu) : 94.42079 90.45745 88.48187 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 183793 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23532 grid for indexing accessible points = 1.400000 m= 93936 mr = 133452 m= 33945 mr = 76691 m= 8397 mr = 27236 m= 1311 mr = 6315 m= 59 mr = 894 m= 0 mr = 17 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 3262 time to turn everything in is 1.410000 number of dielectric boundary points 76836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 20303 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) : 1.930586 object centre at (A) : 20.64600 43.39850 15.80750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7606564 -1.8625196E-02 midg,1,midg; midg,igrid,midg 0.6074176 -0.1322146 1,midg,midg; igrid,midg,midg 1.132792 -0.6179031 gauss-seidel spectral radius is 0.9992715 estimated iterations to convergence 292 setup time was (sec) 1.690000 now iterating at: 15:17:36 rms-change max change #iterations 10.40032 411.9242 at 10iterations 6.128976 147.9478 at 20iterations 3.589971 76.39732 at 30iterations 2.095536 48.81529 at 40iterations 1.218275 24.04679 at 50iterations 0.7102695 12.16951 at 60iterations 0.4124430 7.427738 at 70iterations 0.2396547 4.460835 at 80iterations 0.1389123 2.553259 at 90iterations 8.0644079E-02 1.535281 at 100iterations 4.6832189E-02 0.8060241 at 110iterations 2.7183762E-02 0.4641304 at 120iterations 1.5791437E-02 0.2980187 at 130iterations 9.2071602E-03 0.1580763 at 140iterations 5.4062451E-03 9.1798782E-02 at 150iterations 3.2127777E-03 5.6526184E-02 at 160iterations 1.9486550E-03 3.7628174E-02 at 170iterations 1.2235106E-03 2.4132729E-02 at 180iterations finished qdiffx linear iterations at : 15:17:46 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 1.2235106E-03 2.4132729E-02 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 15:17:46 11.559u 0.191s 0:12.12 96.8% 0+0k 0+0io 0pf+0w