Sun Oct 9 08:15:38 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 Sun Oct 9 2011 at 08:15:38 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: 355 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4167 !!! WARNING: NDP 2113 has a net charge of -3.0000 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: 0.3286862 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): -28.02000 80.29000 ymin,ymax (A): -40.84200 24.62400 zmin,zma (A): -16.78400 83.00500 x,y,z range (A): 108.3100 65.46600 99.78900 scale (grids/A): 0.3286862 object centre (A): 26.13500 -8.108999 33.11050 number of atom coordinates read : 4167 total number of charged atoms : 3687 net assigned charge : 7.500025 assigned positive charge : 576.6571 centred at (gu) : 81.64642 91.74139 85.13669 assigned negative charge : -569.1598 centred at (gu) : 81.61913 91.65969 85.26345 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 2582 nv = 96 ne = 84 npr = 79735 no. pairs analyzed = 79735 no. exposed pairs = 5874 no. arc points = 43771 no. surface atoms = 1967 nbur = 2200 mkacc time = 0.1400000 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 = 2.520000 m= 44 mr = 927 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 1699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2144 ## 715 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 3369 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0605669E-14 -1.4355820E-16 midg,1,midg; midg,igrid,midg -2.6030982E-16 2.0779732E-15 1,midg,midg; igrid,midg,midg -9.4258144E-16 2.2746686E-17 gauss-seidel spectral radius is 0.9534234 estimated iterations to convergence 39 setup time was (sec) 0.4500000 now iterating at: 08:15:39 rms-change max change #iterations 5.1432881E-03 1.798571 at 10iterations 1.6572284E-04 5.7717323E-02 at 20iterations 1.5100247E-05 4.9190521E-03 at 30iterations 1.5758352E-06 5.0067902E-04 at 40iterations 1.7484510E-07 7.0571899E-05 at 50iterations finished qdiffx linear iterations at : 08:15:43 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 1.7484510E-07 7.0571899E-05 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 08:15:43 4.327u 0.178s 0:04.79 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 Sun Oct 9 2011 at 08:15:43 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: 355 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4167 !!! WARNING: NDP 2113 has a net charge of -3.0000 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: 0.9860585 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): -28.02000 80.29000 ymin,ymax (A): -40.84200 24.62400 zmin,zma (A): -16.78400 83.00500 x,y,z range (A): 108.3100 65.46600 99.78900 scale (grids/A): 0.9860585 object centre (A): 26.13500 -8.108999 33.11050 number of atom coordinates read : 4167 total number of charged atoms : 3687 net assigned charge : 7.500025 assigned positive charge : 576.6571 centred at (gu) : 64.93797 95.22317 75.40878 assigned negative charge : -569.1598 centred at (gu) : 64.85699 94.97852 75.79021 start vw surface at 0.1100000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 31406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43771 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.352000 m= 4134 mr = 17609 m= 72 mr = 1604 m= 0 mr = 2 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 399 time to turn everything in is 0.2200000 number of dielectric boundary points 16397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1173 ## 96 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 21484 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) : 0.3286862 object centre at (A) : 26.13500 -8.108999 33.11050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4396253E-04 -4.5891551E-04 midg,1,midg; midg,igrid,midg -1.2703349E-05 4.6737372E-05 1,midg,midg; igrid,midg,midg 3.5957879E-04 4.6311502E-06 gauss-seidel spectral radius is 0.9947938 estimated iterations to convergence 111 setup time was (sec) 0.4300000 now iterating at: 08:15:44 rms-change max change #iterations 0.9707440 117.5312 at 10iterations 0.2201919 19.52516 at 20iterations 5.0396595E-02 4.050831 at 30iterations 1.1431971E-02 0.7627220 at 40iterations 2.6119228E-03 0.1653137 at 50iterations 6.1609561E-04 3.9638400E-02 at 60iterations 1.5461021E-04 9.6416473E-03 at 70iterations 4.3621370E-05 2.8514862E-03 at 80iterations 1.5129081E-05 9.2148781E-04 at 90iterations 5.9970689E-06 3.4856796E-04 at 100iterations 2.5216764E-06 1.5449524E-04 at 110iterations 1.1165851E-06 6.8664551E-05 at 120iterations finished qdiffx linear iterations at : 08:15:51 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 1.1165851E-06 6.8664551E-05 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 08:15:51 7.383u 0.178s 0:07.90 95.5% 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 Sun Oct 9 2011 at 08:15:51 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: 355 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4167 !!! WARNING: NDP 2113 has a net charge of -3.0000 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: 1.479088 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): -28.02000 80.29000 ymin,ymax (A): -40.84200 24.62400 zmin,zma (A): -16.78400 83.00500 x,y,z range (A): 108.3100 65.46600 99.78900 scale (grids/A): 1.479088 object centre (A): 26.13500 -8.108999 33.11050 number of atom coordinates read : 4167 total number of charged atoms : 3687 net assigned charge : 7.500025 assigned positive charge : 576.6571 centred at (gu) : 52.40680 97.83452 68.11287 assigned negative charge : -569.1598 centred at (gu) : 52.28542 97.46771 68.68517 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 74453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43771 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.324000 m= 18767 mr = 45456 m= 1290 mr = 11499 m= 29 mr = 414 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1380 time to turn everything in is 0.4300000 number of dielectric boundary points 37170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 494 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 27437 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) : 0.9860585 object centre at (A) : 26.13500 -8.108999 33.11050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7378531E-02 -9.3933307E-03 midg,1,midg; midg,igrid,midg -2.1421392E-05 1.7293827E-03 1,midg,midg; igrid,midg,midg -0.1011632 2.1076227E-04 gauss-seidel spectral radius is 0.9976728 estimated iterations to convergence 165 setup time was (sec) 0.6600000 now iterating at: 08:15:52 rms-change max change #iterations 3.586288 214.8266 at 10iterations 1.400508 83.66669 at 20iterations 0.5411721 31.59873 at 30iterations 0.2064453 8.994634 at 40iterations 7.8463040E-02 3.081926 at 50iterations 2.9643359E-02 1.341565 at 60iterations 1.1200732E-02 0.4806088 at 70iterations 4.2049419E-03 0.1906099 at 80iterations 1.5778232E-03 6.3625336E-02 at 90iterations 5.9111684E-04 2.8119087E-02 at 100iterations 2.2167224E-04 8.2569122E-03 at 110iterations 8.3307183E-05 3.1929016E-03 at 120iterations 3.1166343E-05 1.1243820E-03 at 130iterations 1.1687533E-05 5.0830841E-04 at 140iterations 4.4532621E-06 1.6593933E-04 at 150iterations 1.8206356E-06 6.6757202E-05 at 160iterations 1.0002649E-06 9.1552734E-05 at 170iterations 8.2041362E-07 9.1552734E-05 at 180iterations finished qdiffx linear iterations at : 08:16:03 total time elapsed so far: 11.20000 # loops : 180 mean,max change (kT/e) : 8.2041362E-07 9.1552734E-05 energy calculations done at 11.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.33000 DelPhi exited at 08:16:03 11.330u 0.192s 0:11.86 97.1% 0+0k 0+0io 0pf+0w