Mon Oct 10 19:33:57 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 Mon Oct 10 2011 at 19:33:57 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4353 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5114061 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): -16.62300 36.41800 ymin,ymax (A): -31.99100 31.44100 zmin,zma (A): -3.745000 65.86700 x,y,z range (A): 53.04100 63.43200 69.61200 scale (grids/A): 0.5114061 object centre (A): 9.897502 -0.2750006 31.06100 number of atom coordinates read : 4353 total number of charged atoms : 4147 net assigned charge : -1.193977 assigned positive charge : 650.7461 centred at (gu) : 90.35087 90.70818 87.60392 assigned negative charge : -651.9442 centred at (gu) : 90.21519 90.76094 87.73004 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7160 nv = 96 ne = 84 npr = 88823 no. pairs analyzed = 88823 no. exposed pairs = 5756 no. arc points = 39579 no. surface atoms = 1914 nbur = 2439 mkacc time = 0.2100000 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 = 1.680000 m= 257 mr = 3573 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3833 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3824 ## 554 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9656 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2969529E-10 -1.7974577E-10 midg,1,midg; midg,igrid,midg 8.4327184E-11 -1.8701307E-10 1,midg,midg; igrid,midg,midg -3.2938260E-10 3.2812558E-10 gauss-seidel spectral radius is 0.9804156 estimated iterations to convergence 59 setup time was (sec) 0.6900000 now iterating at: 19:33:58 rms-change max change #iterations 6.4750485E-02 10.31169 at 10iterations 3.7339055E-03 0.6646214 at 20iterations 3.2412424E-04 4.3317795E-02 at 30iterations 9.1951064E-05 1.4094114E-02 at 40iterations 3.3964599E-05 5.2390099E-03 at 50iterations finished qdiffx linear iterations at : 19:34:01 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 3.3964599E-05 5.2390099E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 19:34:01 3.724u 0.211s 0:04.62 85.0% 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 Mon Oct 10 2011 at 19:34:02 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4353 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.534218 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): -16.62300 36.41800 ymin,ymax (A): -31.99100 31.44100 zmin,zma (A): -3.745000 65.86700 x,y,z range (A): 53.04100 63.43200 69.61200 scale (grids/A): 1.534218 object centre (A): 9.897502 -0.2750006 31.06100 number of atom coordinates read : 4353 total number of charged atoms : 4147 net assigned charge : -1.193977 assigned positive charge : 650.7461 centred at (gu) : 91.05128 92.12328 82.81049 assigned negative charge : -651.9442 centred at (gu) : 90.64513 92.28253 83.18989 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 80484 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39579 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22718 mr = 54098 m= 1940 mr = 14593 m= 44 mr = 736 m= 0 mr = 2 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 67 time to turn everything in is 0.6400000 number of dielectric boundary points 35757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 491 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 31150 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) : 0.5114061 object centre at (A) : 9.897502 -0.2750006 31.06100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7238300E-03 -1.4181891E-02 midg,1,midg; midg,igrid,midg -3.9966265E-03 -1.4768781E-02 1,midg,midg; igrid,midg,midg -3.8914052E-03 1.0291642E-02 gauss-seidel spectral radius is 0.9980767 estimated iterations to convergence 181 setup time was (sec) 0.9600000 now iterating at: 19:34:03 rms-change max change #iterations 3.599009 156.9444 at 10iterations 1.456245 52.76249 at 20iterations 0.5907316 20.01967 at 30iterations 0.2398437 8.500942 at 40iterations 9.7522780E-02 3.333521 at 50iterations 3.9765250E-02 1.404175 at 60iterations 1.6107108E-02 0.5347748 at 70iterations 6.5925089E-03 0.2469615 at 80iterations 2.6982732E-03 8.6421490E-02 at 90iterations 1.1162098E-03 4.1906357E-02 at 100iterations 4.6825522E-04 1.5825272E-02 at 110iterations 2.0823117E-04 7.1487427E-03 at 120iterations finished qdiffx linear iterations at : 19:34:10 total time elapsed so far: 8.120000 # loops : 120 mean,max change (kT/e) : 2.0823117E-04 7.1487427E-03 energy calculations done at 8.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.310000 DelPhi exited at 19:34:11 8.318u 0.257s 0:09.14 93.6% 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 Mon Oct 10 2011 at 19:34:11 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4353 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.301327 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): -16.62300 36.41800 ymin,ymax (A): -31.99100 31.44100 zmin,zma (A): -3.745000 65.86700 x,y,z range (A): 53.04100 63.43200 69.61200 scale (grids/A): 2.301327 object centre (A): 9.897502 -0.2750006 31.06100 number of atom coordinates read : 4353 total number of charged atoms : 4147 net assigned charge : -1.193977 assigned positive charge : 650.7461 centred at (gu) : 91.57661 93.18453 79.21541 assigned negative charge : -651.9442 centred at (gu) : 90.96770 93.42377 79.78471 start vw surface at 0.2100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 187476 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39579 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 81757 mr = 133357 m= 20183 mr = 62633 m= 2669 mr = 13892 m= 144 mr = 1542 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 297 time to turn everything in is 1.480000 number of dielectric boundary points 80761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 33083 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) : 1.534218 object centre at (A) : 9.897502 -0.2750006 31.06100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1699948 -0.2988333 midg,1,midg; midg,igrid,midg -0.1626076 -0.3422675 1,midg,midg; igrid,midg,midg -5.3558290E-02 0.1578229 gauss-seidel spectral radius is 0.9991438 estimated iterations to convergence 270 setup time was (sec) 1.830000 now iterating at: 19:34:13 rms-change max change #iterations 9.828888 260.4561 at 10iterations 5.610506 171.1573 at 20iterations 3.180723 71.04078 at 30iterations 1.793603 45.79294 at 40iterations 1.009592 25.53284 at 50iterations 0.5627927 12.60205 at 60iterations 0.3144294 7.294886 at 70iterations 0.1746745 3.970833 at 80iterations 9.7216271E-02 2.150974 at 90iterations 5.3915989E-02 1.180684 at 100iterations 2.9859118E-02 0.6252723 at 110iterations 1.6566230E-02 0.3302851 at 120iterations 9.1739381E-03 0.2006702 at 130iterations 5.0811656E-03 0.1065917 at 140iterations 2.8175705E-03 5.4758072E-02 at 150iterations 1.5705468E-03 3.1382561E-02 at 160iterations 8.8385865E-04 1.8501282E-02 at 170iterations 5.0544349E-04 1.1272073E-02 at 180iterations finished qdiffx linear iterations at : 19:34:24 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 5.0544349E-04 1.1272073E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 19:34:25 13.334u 0.220s 0:14.13 95.8% 0+0k 0+0io 0pf+0w