Tue Oct 11 06:33:54 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 06:33:55 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7223733 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): -40.77900 -1.429000 ymin,ymax (A): -27.10500 17.66700 zmin,zma (A): -14.90600 34.37600 x,y,z range (A): 39.35000 44.77200 49.28200 scale (grids/A): 0.7223733 object centre (A): -21.10400 -4.719000 9.735000 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 319.9760 centred at (gu) : 91.39759 90.19612 89.00304 assigned negative charge : -314.0311 centred at (gu) : 91.44279 90.33946 88.94186 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7388 nv = 96 ne = 84 npr = 42229 no. pairs analyzed = 42229 no. exposed pairs = 2521 no. arc points = 17094 no. surface atoms = 854 nbur = 1235 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 488 mr = 4288 m= 5 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1560 ## 115 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8055 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5065387E-08 9.4383836E-08 midg,1,midg; midg,igrid,midg 1.6294869E-07 -2.9263466E-08 1,midg,midg; igrid,midg,midg 7.9321133E-08 5.2165714E-08 gauss-seidel spectral radius is 0.9900063 estimated iterations to convergence 81 setup time was (sec) 0.4800000 now iterating at: 06:33:55 rms-change max change #iterations 0.2175897 27.33869 at 10iterations 2.8911298E-02 3.650623 at 20iterations 4.0691937E-03 0.5403891 at 30iterations 6.7444396E-04 9.2529297E-02 at 40iterations 1.6042322E-04 1.8592834E-02 at 50iterations finished qdiffx linear iterations at : 06:33:58 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.6042322E-04 1.8592834E-02 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 06:33:58 3.091u 0.140s 0:03.72 86.8% 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 06:33:58 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.167120 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): -40.77900 -1.429000 ymin,ymax (A): -27.10500 17.66700 zmin,zma (A): -14.90600 34.37600 x,y,z range (A): 39.35000 44.77200 49.28200 scale (grids/A): 2.167120 object centre (A): -21.10400 -4.719000 9.735000 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 319.9760 centred at (gu) : 94.19274 90.58849 87.00912 assigned negative charge : -314.0311 centred at (gu) : 94.32851 91.01840 86.82561 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 78141 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17094 grid for indexing accessible points = 1.400000 m= 31844 mr = 55849 m= 6553 mr = 24473 m= 625 mr = 4409 m= 19 mr = 359 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 32092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15520 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) : 0.7223733 object centre at (A) : -21.10400 -4.719000 9.735000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1007668E-02 3.8659688E-02 midg,1,midg; midg,igrid,midg 4.5705654E-02 -8.8435586E-04 1,midg,midg; igrid,midg,midg 2.0340977E-02 3.1112719E-02 gauss-seidel spectral radius is 0.9988706 estimated iterations to convergence 235 setup time was (sec) 0.8000000 now iterating at: 06:33:59 rms-change max change #iterations 4.822777 202.8674 at 10iterations 2.417105 75.03806 at 20iterations 1.219138 41.04368 at 30iterations 0.6145447 17.63584 at 40iterations 0.3081431 9.446198 at 50iterations 0.1552921 4.486464 at 60iterations 7.7762328E-02 2.275410 at 70iterations 3.9223421E-02 1.156372 at 80iterations 1.9870037E-02 0.5839272 at 90iterations 1.0148703E-02 0.3037932 at 100iterations 5.1833796E-03 0.1462173 at 110iterations 2.7029186E-03 7.7724457E-02 at 120iterations finished qdiffx linear iterations at : 06:34:05 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 2.7029186E-03 7.7724457E-02 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 06:34:06 6.975u 0.173s 0:07.50 95.2% 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 06:34:06 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.250680 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): -40.77900 -1.429000 ymin,ymax (A): -27.10500 17.66700 zmin,zma (A): -14.90600 34.37600 x,y,z range (A): 39.35000 44.77200 49.28200 scale (grids/A): 3.250680 object centre (A): -21.10400 -4.719000 9.735000 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 319.9760 centred at (gu) : 96.28905 90.88266 85.51375 assigned negative charge : -314.0311 centred at (gu) : 96.49291 91.52769 85.23840 start vw surface at 0.1400000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 179982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17094 grid for indexing accessible points = 1.400000 m= 98582 mr = 134289 m= 41278 mr = 82515 m= 12448 mr = 34185 m= 2655 mr = 9738 m= 361 mr = 1996 m= 15 mr = 250 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.780000 number of dielectric boundary points 72348 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 15636 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) : 2.167120 object centre at (A) : -21.10400 -4.719000 9.735000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3269941 0.1411791 midg,1,midg; midg,igrid,midg 0.3507685 -3.6774632E-02 1,midg,midg; igrid,midg,midg 0.1661625 0.3094095 gauss-seidel spectral radius is 0.9993054 estimated iterations to convergence 299 setup time was (sec) 2.050000 now iterating at: 06:34:08 rms-change max change #iterations 10.65250 328.2506 at 10iterations 6.323477 131.5415 at 20iterations 3.737447 80.10571 at 30iterations 2.210129 45.33006 at 40iterations 1.303230 25.14319 at 50iterations 0.7678935 14.49755 at 60iterations 0.4513578 7.228592 at 70iterations 0.2652146 5.403098 at 80iterations 0.1561294 3.144588 at 90iterations 9.2106141E-02 1.632849 at 100iterations 5.4327000E-02 0.9729452 at 110iterations 3.2270275E-02 0.5302792 at 120iterations 1.9331515E-02 0.3408413 at 130iterations 1.1847443E-02 0.2008629 at 140iterations 7.4776071E-03 0.1479950 at 150iterations 4.9487264E-03 9.6843719E-02 at 160iterations 3.4630261E-03 6.6383362E-02 at 170iterations 2.5637329E-03 4.7130585E-02 at 180iterations finished qdiffx linear iterations at : 06:34:17 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 2.5637329E-03 4.7130585E-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 06:34:18 11.564u 0.220s 0:12.31 95.6% 0+0k 0+0io 0pf+0w