Mon Oct 10 20:17:24 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+sph.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 = amb.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 Mon Oct 10 2011 at 20:17:24 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2772 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6290197 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): -10.47300 45.38100 ymin,ymax (A): 27.85400 84.03900 zmin,zma (A): -11.13000 45.46600 x,y,z range (A): 55.85400 56.18500 56.59600 scale (grids/A): 0.6290197 object centre (A): 17.45400 55.94650 17.16800 number of atom coordinates read : 2772 total number of charged atoms : 2633 net assigned charge : -0.4999801 assigned positive charge : 410.9646 centred at (gu) : 89.31520 90.38020 89.72625 assigned negative charge : -411.4657 centred at (gu) : 89.36525 90.32953 89.80048 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7424 nv = 96 ne = 84 npr = 54811 no. pairs analyzed = 54811 no. exposed pairs = 3938 no. arc points = 28077 no. surface atoms = 1299 nbur = 1473 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3554 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2658 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8897 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5019830E-09 -6.9920785E-09 midg,1,midg; midg,igrid,midg -4.8273958E-09 4.3528483E-09 1,midg,midg; igrid,midg,midg 4.5953943E-09 -4.4659858E-09 gauss-seidel spectral radius is 0.9869384 estimated iterations to convergence 72 setup time was (sec) 0.3800000 now iterating at: 20:17:25 rms-change max change #iterations 0.1390766 22.48116 at 10iterations 1.2845118E-02 2.164453 at 20iterations 1.2297558E-03 0.2022228 at 30iterations 1.1533804E-04 1.6407847E-02 at 40iterations 1.1124156E-05 1.4953613E-03 at 50iterations finished qdiffx linear iterations at : 20:17:28 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.1124156E-05 1.4953613E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 20:17:28 3.372u 0.177s 0:04.09 86.5% 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 Mon Oct 10 2011 at 20:17:28 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2772 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.887059 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): -10.47300 45.38100 ymin,ymax (A): 27.85400 84.03900 zmin,zma (A): -11.13000 45.46600 x,y,z range (A): 55.85400 56.18500 56.59600 scale (grids/A): 1.887059 object centre (A): 17.45400 55.94650 17.16800 number of atom coordinates read : 2772 total number of charged atoms : 2633 net assigned charge : -0.4999801 assigned positive charge : 410.9646 centred at (gu) : 87.94526 91.13992 89.17848 assigned negative charge : -411.4657 centred at (gu) : 88.09547 90.98795 89.40128 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28077 grid for indexing accessible points = 1.400000 m= 27550 mr = 50871 m= 4450 mr = 18712 m= 254 mr = 2435 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 39119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20714 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) : 0.6290197 object centre at (A) : 17.45400 55.94650 17.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3158082E-03 -4.5344546E-02 midg,1,midg; midg,igrid,midg 2.2211676E-02 3.2522693E-02 1,midg,midg; igrid,midg,midg 8.4569762E-03 -1.0806277E-02 gauss-seidel spectral radius is 0.9986499 estimated iterations to convergence 216 setup time was (sec) 0.6100000 now iterating at: 20:17:29 rms-change max change #iterations 4.305340 197.5543 at 10iterations 2.011646 68.89340 at 20iterations 0.9455970 28.82375 at 30iterations 0.4421632 13.86736 at 40iterations 0.2071730 6.386267 at 50iterations 9.6971624E-02 3.026337 at 60iterations 4.5629084E-02 1.397477 at 70iterations 2.1391949E-02 0.6386499 at 80iterations 1.0049622E-02 0.3175435 at 90iterations 4.7244183E-03 0.1536121 at 100iterations 2.2182546E-03 6.8391800E-02 at 110iterations 1.0423410E-03 3.2974243E-02 at 120iterations finished qdiffx linear iterations at : 20:17:36 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 1.0423410E-03 3.2974243E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 20:17:37 7.849u 0.205s 0:08.51 94.4% 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 Mon Oct 10 2011 at 20:17:37 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2772 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.830589 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): -10.47300 45.38100 ymin,ymax (A): 27.85400 84.03900 zmin,zma (A): -11.13000 45.46600 x,y,z range (A): 55.85400 56.18500 56.59600 scale (grids/A): 2.830589 object centre (A): 17.45400 55.94650 17.16800 number of atom coordinates read : 2772 total number of charged atoms : 2633 net assigned charge : -0.4999801 assigned positive charge : 410.9646 centred at (gu) : 86.91764 91.70993 88.76743 assigned negative charge : -411.4657 centred at (gu) : 87.14322 91.48175 89.10204 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 182243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28077 grid for indexing accessible points = 1.400000 m= 87696 mr = 124598 m= 32222 mr = 67893 m= 7855 mr = 24463 m= 1125 mr = 5390 m= 38 mr = 640 m= 0 mr = 3 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.020000 number of dielectric boundary points 88192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 21062 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) : 1.887059 object centre at (A) : 17.45400 55.94650 17.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9072678E-03 -0.4433392 midg,1,midg; midg,igrid,midg 0.2789375 0.5411497 1,midg,midg; igrid,midg,midg 0.2896744 -0.1227184 gauss-seidel spectral radius is 0.9992853 estimated iterations to convergence 295 setup time was (sec) 1.260000 now iterating at: 20:17:38 rms-change max change #iterations 10.45572 364.2847 at 10iterations 6.258472 150.4581 at 20iterations 3.731884 92.56833 at 30iterations 2.205603 52.34273 at 40iterations 1.297689 23.94595 at 50iterations 0.7622451 14.53646 at 60iterations 0.4461726 8.557963 at 70iterations 0.2606838 4.933038 at 80iterations 0.1520389 2.820789 at 90iterations 8.8542923E-02 1.589714 at 100iterations 5.1739868E-02 0.9931951 at 110iterations 3.0086527E-02 0.5332818 at 120iterations 1.7515060E-02 0.3339815 at 130iterations 1.0164005E-02 0.1812878 at 140iterations 5.9038317E-03 0.1018410 at 150iterations 3.4302641E-03 6.5797806E-02 at 160iterations 1.9915195E-03 3.3050537E-02 at 170iterations 1.1584437E-03 1.9968033E-02 at 180iterations finished qdiffx linear iterations at : 20:17:50 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 1.1584437E-03 1.9968033E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 20:17:50 12.896u 0.213s 0:13.42 97.6% 0+0k 0+0io 0pf+0w