Sun Oct 9 13:01:00 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 13:01:00 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6827248 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): -7.583000 44.56100 ymin,ymax (A): -13.90800 36.91000 zmin,zma (A): 2.575000 44.91100 x,y,z range (A): 52.14400 50.81800 42.33600 scale (grids/A): 0.6827248 object centre (A): 18.48900 11.50100 23.74300 number of atom coordinates read : 2367 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 89.99371 91.36232 90.70853 assigned negative charge : -356.4896 centred at (gu) : 90.01164 91.51637 90.74440 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7596 nv = 96 ne = 84 npr = 47260 no. pairs analyzed = 47260 no. exposed pairs = 2935 no. arc points = 20961 no. surface atoms = 993 nbur = 1374 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 455 mr = 4220 m= 3 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2017 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8486 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4630806E-08 6.2363612E-09 midg,1,midg; midg,igrid,midg 4.9586667E-08 -4.3954341E-08 1,midg,midg; igrid,midg,midg 2.2703842E-08 1.1246127E-08 gauss-seidel spectral radius is 0.9888570 estimated iterations to convergence 77 setup time was (sec) 0.4900000 now iterating at: 13:01:01 rms-change max change #iterations 0.1832522 27.96241 at 10iterations 2.1600841E-02 3.416677 at 20iterations 3.0104702E-03 0.4351425 at 30iterations 6.9659972E-04 0.1080017 at 40iterations 2.3136707E-04 3.6483765E-02 at 50iterations finished qdiffx linear iterations at : 13:01:03 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 2.3136707E-04 3.6483765E-02 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 13:01:04 3.100u 0.138s 0:03.50 92.2% 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 13:01:04 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 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: 2.048174 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): -7.583000 44.56100 ymin,ymax (A): -13.90800 36.91000 zmin,zma (A): 2.575000 44.91100 x,y,z range (A): 52.14400 50.81800 42.33600 scale (grids/A): 2.048174 object centre (A): 18.48900 11.50100 23.74300 number of atom coordinates read : 2367 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 89.98054 94.08655 92.12489 assigned negative charge : -356.4896 centred at (gu) : 90.03484 94.54911 92.23285 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 79773 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20961 grid for indexing accessible points = 1.400000 m= 31528 mr = 55180 m= 5567 mr = 23786 m= 433 mr = 3603 m= 14 mr = 199 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 0.5400000 number of dielectric boundary points 34547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17634 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) : 0.6827248 object centre at (A) : 18.48900 11.50100 23.74300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1755065E-02 8.7900357E-03 midg,1,midg; midg,igrid,midg 1.5641574E-02 -3.5888713E-02 1,midg,midg; igrid,midg,midg 4.8193537E-02 -8.5872104E-03 gauss-seidel spectral radius is 0.9987944 estimated iterations to convergence 228 setup time was (sec) 0.8200000 now iterating at: 13:01:05 rms-change max change #iterations 4.665460 227.4431 at 10iterations 2.275916 79.24972 at 20iterations 1.117464 37.05831 at 30iterations 0.5487620 17.35013 at 40iterations 0.2689412 8.765121 at 50iterations 0.1316737 3.755037 at 60iterations 6.5038897E-02 1.871843 at 70iterations 3.1995542E-02 0.9400514 at 80iterations 1.5897455E-02 0.4682513 at 90iterations 7.9238517E-03 0.2408562 at 100iterations 4.0476210E-03 0.1270366 at 110iterations 2.1395034E-03 7.2601318E-02 at 120iterations finished qdiffx linear iterations at : 13:01:10 total time elapsed so far: 6.730000 # loops : 120 mean,max change (kT/e) : 2.1395034E-03 7.2601318E-02 energy calculations done at 6.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.910000 DelPhi exited at 13:01:11 6.909u 0.145s 0:07.38 95.3% 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 13:01:11 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 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: 3.072262 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): -7.583000 44.56100 ymin,ymax (A): -13.90800 36.91000 zmin,zma (A): 2.575000 44.91100 x,y,z range (A): 52.14400 50.81800 42.33600 scale (grids/A): 3.072262 object centre (A): 18.48900 11.50100 23.74300 number of atom coordinates read : 2367 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 89.97083 96.12987 93.18726 assigned negative charge : -356.4896 centred at (gu) : 90.05227 96.82365 93.34911 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 183822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20961 grid for indexing accessible points = 1.400000 m= 98266 mr = 133163 m= 39133 mr = 81218 m= 10245 mr = 31973 m= 1848 mr = 7902 m= 171 mr = 1293 m= 5 mr = 80 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 1.420000 number of dielectric boundary points 77861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 17798 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) : 2.048174 object centre at (A) : 18.48900 11.50100 23.74300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4375634 -1.5471541E-02 midg,1,midg; midg,igrid,midg 0.3454593 -0.4362916 1,midg,midg; igrid,midg,midg 0.4622658 -0.4483791 gauss-seidel spectral radius is 0.9992905 estimated iterations to convergence 296 setup time was (sec) 1.700000 now iterating at: 13:01:13 rms-change max change #iterations 10.57474 400.7089 at 10iterations 6.254157 120.8793 at 20iterations 3.679392 73.61190 at 30iterations 2.170938 43.57327 at 40iterations 1.275405 24.28154 at 50iterations 0.7458284 17.49361 at 60iterations 0.4372430 8.347380 at 70iterations 0.2558344 4.958799 at 80iterations 0.1495131 2.553455 at 90iterations 8.7612040E-02 1.502556 at 100iterations 5.1152013E-02 0.8883166 at 110iterations 3.0069849E-02 0.5225830 at 120iterations 1.7766604E-02 0.3306379 at 130iterations 1.0650875E-02 0.1898346 at 140iterations 6.5719830E-03 0.1359901 at 150iterations 4.2089806E-03 8.2897186E-02 at 160iterations 2.8607156E-03 6.1391830E-02 at 170iterations 2.0771977E-03 4.3708801E-02 at 180iterations finished qdiffx linear iterations at : 13:01:22 total time elapsed so far: 11.04000 # loops : 180 mean,max change (kT/e) : 2.0771977E-03 4.3708801E-02 energy calculations done at 11.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.22000 DelPhi exited at 13:01:23 11.225u 0.183s 0:11.70 97.4% 0+0k 0+0io 0pf+0w