Sun Oct 9 12:00:05 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 12:00:05 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 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: 0.6978750 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): -6.376000 44.10900 ymin,ymax (A): -14.19400 36.81800 zmin,zma (A): 1.538000 44.64100 x,y,z range (A): 50.48500 51.01200 43.10300 scale (grids/A): 0.6978750 object centre (A): 18.86650 11.31200 23.08950 number of atom coordinates read : 2380 total number of charged atoms : 2239 net assigned charge : 4.500015 assigned positive charge : 366.1681 centred at (gu) : 89.51418 91.09815 90.90141 assigned negative charge : -361.6685 centred at (gu) : 89.52420 91.24152 90.99358 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7776 nv = 96 ne = 84 npr = 48127 no. pairs analyzed = 48127 no. exposed pairs = 2915 no. arc points = 20657 no. surface atoms = 987 nbur = 1393 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 506 mr = 4350 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.2800000 number of dielectric boundary points 3857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1902 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8804 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1571981E-08 -1.4114685E-08 midg,1,midg; midg,igrid,midg 7.7728771E-08 -4.4991300E-08 1,midg,midg; igrid,midg,midg 3.9574914E-08 2.4459565E-08 gauss-seidel spectral radius is 0.9893299 estimated iterations to convergence 79 setup time was (sec) 0.5200000 now iterating at: 12:00:06 rms-change max change #iterations 0.2074264 33.32281 at 10iterations 2.5308458E-02 3.009056 at 20iterations 3.3592659E-03 0.5381813 at 30iterations 5.8949471E-04 0.1059113 at 40iterations 1.5161968E-04 2.4703979E-02 at 50iterations finished qdiffx linear iterations at : 12:00:08 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.5161968E-04 2.4703979E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 12:00:09 3.366u 0.191s 0:03.83 92.6% 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 12:00:09 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 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: 2.093625 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): -6.376000 44.10900 ymin,ymax (A): -14.19400 36.81800 zmin,zma (A): 1.538000 44.64100 x,y,z range (A): 50.48500 51.01200 43.10300 scale (grids/A): 2.093625 object centre (A): 18.86650 11.31200 23.08950 number of atom coordinates read : 2380 total number of charged atoms : 2239 net assigned charge : 4.500015 assigned positive charge : 366.1681 centred at (gu) : 88.54202 93.29410 92.70390 assigned negative charge : -361.6685 centred at (gu) : 88.57259 93.72421 92.98038 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 82387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20657 grid for indexing accessible points = 1.400000 m= 32474 mr = 57391 m= 6019 mr = 24357 m= 505 mr = 3905 m= 12 mr = 228 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1540 time to turn everything in is 0.5800000 number of dielectric boundary points 35516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17770 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) : 0.6978750 object centre at (A) : 18.86650 11.31200 23.08950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5885797E-02 8.1588334E-04 midg,1,midg; midg,igrid,midg 2.0646229E-02 -3.8140424E-02 1,midg,midg; igrid,midg,midg 3.5602413E-02 -1.4028357E-02 gauss-seidel spectral radius is 0.9988363 estimated iterations to convergence 232 setup time was (sec) 0.8600000 now iterating at: 12:00:10 rms-change max change #iterations 4.924883 216.8481 at 10iterations 2.431036 76.47404 at 20iterations 1.204103 35.15500 at 30iterations 0.5971720 18.04483 at 40iterations 0.2965724 11.82172 at 50iterations 0.1468687 4.416976 at 60iterations 7.3066518E-02 2.033838 at 70iterations 3.6338963E-02 1.091419 at 80iterations 1.8199656E-02 0.5032272 at 90iterations 9.1159493E-03 0.2652683 at 100iterations 4.6067964E-03 0.1312408 at 110iterations 2.3674159E-03 6.5940857E-02 at 120iterations finished qdiffx linear iterations at : 12:00:17 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 2.3674159E-03 6.5940857E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 12:00:17 7.678u 0.253s 0:08.26 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 12:00:17 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 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: 3.140437 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): -6.376000 44.10900 ymin,ymax (A): -14.19400 36.81800 zmin,zma (A): 1.538000 44.64100 x,y,z range (A): 50.48500 51.01200 43.10300 scale (grids/A): 3.140437 object centre (A): 18.86650 11.31200 23.08950 number of atom coordinates read : 2380 total number of charged atoms : 2239 net assigned charge : 4.500015 assigned positive charge : 366.1681 centred at (gu) : 87.81300 94.94098 94.05573 assigned negative charge : -361.6685 centred at (gu) : 87.85876 95.58630 94.47052 start vw surface at 0.1300000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 189741 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20657 grid for indexing accessible points = 1.400000 m= 101610 mr = 138633 m= 40527 mr = 83731 m= 11404 mr = 32828 m= 2214 mr = 8700 m= 263 mr = 1592 m= 13 mr = 176 m= 0 mr = 7 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 5214 time to turn everything in is 1.860000 number of dielectric boundary points 80105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 17912 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) : 2.093625 object centre at (A) : 18.86650 11.31200 23.08950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5665541 -0.1346307 midg,1,midg; midg,igrid,midg 0.4382894 -0.4178059 1,midg,midg; igrid,midg,midg 0.2818586 -0.3855115 gauss-seidel spectral radius is 0.9992993 estimated iterations to convergence 298 setup time was (sec) 2.170000 now iterating at: 12:00:20 rms-change max change #iterations 11.06855 323.1376 at 10iterations 6.563217 139.6323 at 20iterations 3.890886 89.23929 at 30iterations 2.294506 41.44612 at 40iterations 1.353413 23.73964 at 50iterations 0.7971105 13.42105 at 60iterations 0.4687672 8.290434 at 70iterations 0.2748792 4.462114 at 80iterations 0.1614169 2.788532 at 90iterations 9.4596259E-02 1.743833 at 100iterations 5.5524014E-02 0.9065228 at 110iterations 3.2735705E-02 0.5750885 at 120iterations 1.9410109E-02 0.3108578 at 130iterations 1.1619855E-02 0.2048492 at 140iterations 7.1234847E-03 0.1362152 at 150iterations 4.5131687E-03 9.0217590E-02 at 160iterations 2.9931390E-03 6.1809540E-02 at 170iterations 2.1081564E-03 4.5398712E-02 at 180iterations finished qdiffx linear iterations at : 12:00:32 total time elapsed so far: 14.64000 # loops : 180 mean,max change (kT/e) : 2.1081564E-03 4.5398712E-02 energy calculations done at 14.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.82000 DelPhi exited at 12:00:33 14.822u 0.260s 0:15.38 98.0% 0+0k 0+0io 0pf+0w