Sun Oct 9 08:48:34 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 08:48:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5265 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: 0.5174795 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): 8.448999 77.24400 ymin,ymax (A): -30.53600 33.16100 zmin,zma (A): -14.83700 50.52500 x,y,z range (A): 68.79500 63.69700 65.36200 scale (grids/A): 0.5174795 object centre (A): 42.84650 1.312500 17.84400 number of atom coordinates read : 5265 total number of charged atoms : 5102 net assigned charge : -3.499990 assigned positive charge : 790.9142 centred at (gu) : 89.52782 89.80932 88.59415 assigned negative charge : -794.4205 centred at (gu) : 89.42446 89.89361 88.62679 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8899 nv = 96 ne = 84 npr = 107155 no. pairs analyzed = 107155 no. exposed pairs = 6613 no. arc points = 46108 no. surface atoms = 2214 nbur = 3051 mkacc time = 0.2400000 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 = 1.652000 m= 295 mr = 4576 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4514 ## 645 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 11919 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5570710E-11 -1.3463515E-10 midg,1,midg; midg,igrid,midg 2.6672489E-10 -3.7616110E-10 1,midg,midg; igrid,midg,midg -5.3312399E-10 2.8671304E-10 gauss-seidel spectral radius is 0.9809350 estimated iterations to convergence 60 setup time was (sec) 0.7100000 now iterating at: 08:48:35 rms-change max change #iterations 7.6507591E-02 12.73451 at 10iterations 4.4297730E-03 0.5967236 at 20iterations 3.2876048E-04 6.6078186E-02 at 30iterations 6.0565606E-05 1.6408920E-02 at 40iterations 1.7369992E-05 4.5700073E-03 at 50iterations finished qdiffx linear iterations at : 08:48:37 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 1.7369992E-05 4.5700073E-03 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 08:48:38 3.271u 0.139s 0:03.78 89.9% 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 08:48:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5265 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: 1.552438 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): 8.448999 77.24400 ymin,ymax (A): -30.53600 33.16100 zmin,zma (A): -14.83700 50.52500 x,y,z range (A): 68.79500 63.69700 65.36200 scale (grids/A): 1.552438 object centre (A): 42.84650 1.312500 17.84400 number of atom coordinates read : 5265 total number of charged atoms : 5102 net assigned charge : -3.499990 assigned positive charge : 790.9142 centred at (gu) : 88.58171 89.42591 85.78043 assigned negative charge : -794.4205 centred at (gu) : 88.27306 89.68086 85.87983 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 100084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46108 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 28055 mr = 68321 m= 2291 mr = 18157 m= 37 mr = 943 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1347 time to turn everything in is 0.6500000 number of dielectric boundary points 43046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 637 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 38457 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) : 0.5174795 object centre at (A) : 42.84650 1.312500 17.84400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0414852E-02 -1.6127532E-02 midg,1,midg; midg,igrid,midg 1.0948691E-02 -2.4599500E-03 1,midg,midg; igrid,midg,midg -1.9407487E-02 4.1004308E-03 gauss-seidel spectral radius is 0.9982170 estimated iterations to convergence 188 setup time was (sec) 0.9200000 now iterating at: 08:48:39 rms-change max change #iterations 4.125227 158.3331 at 10iterations 1.730995 63.55163 at 20iterations 0.7275454 23.93847 at 30iterations 0.3061476 9.862944 at 40iterations 0.1284475 4.555061 at 50iterations 5.4078951E-02 1.621487 at 60iterations 2.2790367E-02 0.6683276 at 70iterations 9.6122082E-03 0.2972741 at 80iterations 4.0598274E-03 0.1231842 at 90iterations 1.7099875E-03 5.5850029E-02 at 100iterations 7.2976731E-04 2.5623322E-02 at 110iterations 3.1436622E-04 1.2105942E-02 at 120iterations finished qdiffx linear iterations at : 08:48:45 total time elapsed so far: 7.020000 # loops : 120 mean,max change (kT/e) : 3.1436622E-04 1.2105942E-02 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.210000 DelPhi exited at 08:48:46 7.209u 0.201s 0:07.72 95.8% 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 Sun Oct 9 2011 at 08:48:46 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 = 5265 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: 2.328658 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): 8.448999 77.24400 ymin,ymax (A): -30.53600 33.16100 zmin,zma (A): -14.83700 50.52500 x,y,z range (A): 68.79500 63.69700 65.36200 scale (grids/A): 2.328658 object centre (A): 42.84650 1.312500 17.84400 number of atom coordinates read : 5265 total number of charged atoms : 5102 net assigned charge : -3.499990 assigned positive charge : 790.9142 centred at (gu) : 87.87205 89.13834 83.67033 assigned negative charge : -794.4205 centred at (gu) : 87.40961 89.52127 83.81960 start vw surface at 0.2200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 233178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46108 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 101701 mr = 167973 m= 24453 mr = 78321 m= 3186 mr = 17353 m= 150 mr = 1892 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 4575 time to turn everything in is 1.620000 number of dielectric boundary points 97092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 40718 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) : 1.552438 object centre at (A) : 42.84650 1.312500 17.84400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2995736 -0.3961929 midg,1,midg; midg,igrid,midg 0.1465410 -3.2107983E-02 1,midg,midg; igrid,midg,midg -0.4980460 2.5703156E-02 gauss-seidel spectral radius is 0.9992106 estimated iterations to convergence 281 setup time was (sec) 1.920000 now iterating at: 08:48:48 rms-change max change #iterations 11.09354 303.9203 at 10iterations 6.504820 161.9932 at 20iterations 3.773235 75.88539 at 30iterations 2.182910 44.29726 at 40iterations 1.257445 24.90946 at 50iterations 0.7211816 15.91503 at 60iterations 0.4133392 7.547928 at 70iterations 0.2358036 4.255863 at 80iterations 0.1346614 2.588600 at 90iterations 7.6871730E-02 1.322350 at 100iterations 4.3624602E-02 0.8399429 at 110iterations 2.4797961E-02 0.4814893 at 120iterations 1.4107778E-02 0.2468891 at 130iterations 8.0086561E-03 0.1381133 at 140iterations 4.5405226E-03 8.0741405E-02 at 150iterations 2.5783477E-03 4.3286681E-02 at 160iterations 1.4661085E-03 2.6630640E-02 at 170iterations 8.3521655E-04 1.4331818E-02 at 180iterations finished qdiffx linear iterations at : 08:48:57 total time elapsed so far: 11.65000 # loops : 180 mean,max change (kT/e) : 8.3521655E-04 1.4331818E-02 energy calculations done at 11.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.82000 DelPhi exited at 08:48:58 11.822u 0.152s 0:12.24 97.7% 0+0k 0+0io 0pf+0w