Sun Oct 9 09:00:53 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 Sun Oct 9 2011 at 09:00:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5837 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4968112 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): -19.18900 52.46800 ymin,ymax (A): -66.60400 -3.063000 zmin,zma (A): -14.49200 50.55700 x,y,z range (A): 71.65700 63.54100 65.04900 scale (grids/A): 0.4968112 object centre (A): 16.63950 -34.83350 18.03250 number of atom coordinates read : 5837 total number of charged atoms : 5669 net assigned charge : 0.5000427 assigned positive charge : 880.2244 centred at (gu) : 90.32872 90.20180 89.00439 assigned negative charge : -879.7318 centred at (gu) : 90.47779 90.18574 89.00483 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8859 nv = 96 ne = 84 npr = 118879 no. pairs analyzed = 118879 no. exposed pairs = 7173 no. arc points = 49753 no. surface atoms = 2407 nbur = 3430 mkacc time = 0.2600000 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 = 1.708000 m= 295 mr = 4504 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.5200000 number of dielectric boundary points 4646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4863 ## 760 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12168 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2885352E-12 3.1308235E-12 midg,1,midg; midg,igrid,midg -2.1962909E-11 3.4600094E-11 1,midg,midg; igrid,midg,midg 2.3701657E-10 -2.8497096E-10 gauss-seidel spectral radius is 0.9793563 estimated iterations to convergence 58 setup time was (sec) 0.7300000 now iterating at: 09:00:54 rms-change max change #iterations 6.6424578E-02 9.904172 at 10iterations 3.5738165E-03 0.4720850 at 20iterations 3.3093247E-04 7.5160980E-02 at 30iterations 7.5054901E-05 1.7873764E-02 at 40iterations 2.1574011E-05 4.6730042E-03 at 50iterations finished qdiffx linear iterations at : 09:00:57 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 2.1574011E-05 4.6730042E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 09:00:57 3.322u 0.139s 0:03.76 91.7% 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 09:00:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5837 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.490434 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): -19.18900 52.46800 ymin,ymax (A): -66.60400 -3.063000 zmin,zma (A): -14.49200 50.55700 x,y,z range (A): 71.65700 63.54100 65.04900 scale (grids/A): 1.490434 object centre (A): 16.63950 -34.83350 18.03250 number of atom coordinates read : 5837 total number of charged atoms : 5669 net assigned charge : 0.5000427 assigned positive charge : 880.2244 centred at (gu) : 90.98433 90.60342 87.01115 assigned negative charge : -879.7318 centred at (gu) : 91.43302 90.55707 87.01385 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 101232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49753 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27328 mr = 69087 m= 2017 mr = 17536 m= 34 mr = 764 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1527 time to turn everything in is 0.6600000 number of dielectric boundary points 43222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 731 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 42158 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) : 0.4968112 object centre at (A) : 16.63950 -34.83350 18.03250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0808862E-03 -9.9578276E-03 midg,1,midg; midg,igrid,midg 1.7656182E-03 9.2234034E-03 1,midg,midg; igrid,midg,midg 2.7550505E-02 -1.6114492E-02 gauss-seidel spectral radius is 0.9980887 estimated iterations to convergence 182 setup time was (sec) 0.9300000 now iterating at: 09:00:58 rms-change max change #iterations 3.979558 157.6726 at 10iterations 1.627506 53.38220 at 20iterations 0.6625295 19.73203 at 30iterations 0.2702958 8.624216 at 40iterations 0.1106319 3.638766 at 50iterations 4.5163382E-02 1.316368 at 60iterations 1.8448282E-02 0.5949674 at 70iterations 7.5590303E-03 0.2297325 at 80iterations 3.0972778E-03 9.6846581E-02 at 90iterations 1.2781917E-03 3.9768219E-02 at 100iterations 5.3167791E-04 1.7485619E-02 at 110iterations 2.2517590E-04 6.7547560E-03 at 120iterations finished qdiffx linear iterations at : 09:01:05 total time elapsed so far: 7.130000 # loops : 120 mean,max change (kT/e) : 2.2517590E-04 6.7547560E-03 energy calculations done at 7.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.310000 DelPhi exited at 09:01:05 7.309u 0.168s 0:07.75 96.2% 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 Sun Oct 9 2011 at 09:01:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5837 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.235651 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): -19.18900 52.46800 ymin,ymax (A): -66.60400 -3.063000 zmin,zma (A): -14.49200 50.55700 x,y,z range (A): 71.65700 63.54100 65.04900 scale (grids/A): 2.235651 object centre (A): 16.63950 -34.83350 18.03250 number of atom coordinates read : 5837 total number of charged atoms : 5669 net assigned charge : 0.5000427 assigned positive charge : 880.2244 centred at (gu) : 91.47601 90.90489 85.51615 assigned negative charge : -879.7318 centred at (gu) : 92.14941 90.83555 85.52067 start vw surface at 0.2100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 236524 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49753 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 100504 mr = 170710 m= 23141 mr = 77037 m= 2757 mr = 16101 m= 114 mr = 1580 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 4954 time to turn everything in is 1.580000 number of dielectric boundary points 97582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 45160 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) : 1.490434 object centre at (A) : 16.63950 -34.83350 18.03250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2371643 -0.2848132 midg,1,midg; midg,igrid,midg 3.9391514E-02 0.2179448 1,midg,midg; igrid,midg,midg 0.7916842 -0.4463051 gauss-seidel spectral radius is 0.9991828 estimated iterations to convergence 276 setup time was (sec) 1.870000 now iterating at: 09:01:07 rms-change max change #iterations 11.08184 298.4283 at 10iterations 6.430134 138.2290 at 20iterations 3.699784 90.51244 at 30iterations 2.124353 45.82003 at 40iterations 1.212992 26.79913 at 50iterations 0.6891928 12.90630 at 60iterations 0.3915534 8.728951 at 70iterations 0.2221185 4.296890 at 80iterations 0.1254687 2.630613 at 90iterations 7.0906430E-02 1.382348 at 100iterations 3.9988767E-02 0.7305222 at 110iterations 2.2526298E-02 0.4245434 at 120iterations 1.2715785E-02 0.2665820 at 130iterations 7.1461475E-03 0.1265793 at 140iterations 4.0368414E-03 7.2981834E-02 at 150iterations 2.2704985E-03 4.0733337E-02 at 160iterations 1.2804348E-03 2.2832870E-02 at 170iterations 7.2445878E-04 1.2428284E-02 at 180iterations finished qdiffx linear iterations at : 09:01:17 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 7.2445878E-04 1.2428284E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.62000 DelPhi exited at 09:01:17 11.621u 0.163s 0:12.09 97.4% 0+0k 0+0io 0pf+0w