Mon Oct 10 17:16:45 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 Mon Oct 10 2011 at 17:16:45 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4775 !!! WARNING: HEM 819 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: 0.5116634 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): -18.65200 37.46200 ymin,ymax (A): -30.71200 34.09000 zmin,zma (A): -3.947000 65.63000 x,y,z range (A): 56.11400 64.80200 69.57700 scale (grids/A): 0.5116634 object centre (A): 9.405001 1.689000 30.84150 number of atom coordinates read : 4775 total number of charged atoms : 4529 net assigned charge : 6.800046 assigned positive charge : 717.5753 centred at (gu) : 90.09590 90.34891 88.39720 assigned negative charge : -710.7799 centred at (gu) : 89.97965 90.41612 88.39597 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7994 nv = 96 ne = 84 npr = 96090 no. pairs analyzed = 96090 no. exposed pairs = 6006 no. arc points = 42299 no. surface atoms = 2020 nbur = 2755 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 = 1.652000 m= 282 mr = 4133 m= 2 mr = 9 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 0.4400000 number of dielectric boundary points 4136 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4031 ## 589 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 10511 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4838319E-10 6.9842597E-11 midg,1,midg; midg,igrid,midg 2.5640406E-10 -8.9565910E-11 1,midg,midg; igrid,midg,midg -2.1093551E-10 4.2038301E-10 gauss-seidel spectral radius is 0.9804686 estimated iterations to convergence 59 setup time was (sec) 0.6600000 now iterating at: 17:16:46 rms-change max change #iterations 6.9212086E-02 9.956239 at 10iterations 4.2944108E-03 0.6984673 at 20iterations 7.3713111E-04 0.1125774 at 30iterations 2.8067309E-04 4.4318199E-02 at 40iterations 1.1399695E-04 1.7993927E-02 at 50iterations finished qdiffx linear iterations at : 17:16:48 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.1399695E-04 1.7993927E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 17:16:49 3.323u 0.145s 0:03.92 88.2% 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 Mon Oct 10 2011 at 17:16:49 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4775 !!! WARNING: HEM 819 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.534990 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): -18.65200 37.46200 ymin,ymax (A): -30.71200 34.09000 zmin,zma (A): -3.947000 65.63000 x,y,z range (A): 56.11400 64.80200 69.57700 scale (grids/A): 1.534990 object centre (A): 9.405001 1.689000 30.84150 number of atom coordinates read : 4775 total number of charged atoms : 4529 net assigned charge : 6.800046 assigned positive charge : 717.5753 centred at (gu) : 90.28654 91.04552 85.19011 assigned negative charge : -710.7799 centred at (gu) : 89.93863 91.24821 85.18790 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 90391 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42299 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26287 mr = 62171 m= 2328 mr = 17405 m= 48 mr = 965 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 38513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 590 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 33970 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) : 0.5116634 object centre at (A) : 9.405001 1.689000 30.84150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2973814E-03 1.6697416E-02 midg,1,midg; midg,igrid,midg 1.3815528E-02 -1.2285712E-02 1,midg,midg; igrid,midg,midg -1.9885208E-03 1.2348987E-02 gauss-seidel spectral radius is 0.9981254 estimated iterations to convergence 184 setup time was (sec) 0.9000000 now iterating at: 17:16:50 rms-change max change #iterations 3.795956 150.5043 at 10iterations 1.562096 51.81984 at 20iterations 0.6439825 23.22469 at 30iterations 0.2651750 8.406921 at 40iterations 0.1092557 3.542305 at 50iterations 4.5120981E-02 1.413126 at 60iterations 1.8614450E-02 0.5990067 at 70iterations 7.7397819E-03 0.2533188 at 80iterations 3.2816171E-03 0.1161098 at 90iterations 1.4414759E-03 5.0175190E-02 at 100iterations 7.0234551E-04 2.7887076E-02 at 110iterations 3.9593285E-04 1.5029907E-02 at 120iterations finished qdiffx linear iterations at : 17:16:56 total time elapsed so far: 7.090000 # loops : 120 mean,max change (kT/e) : 3.9593285E-04 1.5029907E-02 energy calculations done at 7.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.260000 DelPhi exited at 17:16:57 7.263u 0.208s 0:07.76 96.1% 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 17:16:57 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4775 !!! WARNING: HEM 819 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: 2.302485 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): -18.65200 37.46200 ymin,ymax (A): -30.71200 34.09000 zmin,zma (A): -3.947000 65.63000 x,y,z range (A): 56.11400 64.80200 69.57700 scale (grids/A): 2.302485 object centre (A): 9.405001 1.689000 30.84150 number of atom coordinates read : 4775 total number of charged atoms : 4529 net assigned charge : 6.800046 assigned positive charge : 717.5753 centred at (gu) : 90.42941 91.56792 82.78487 assigned negative charge : -710.7799 centred at (gu) : 89.90781 91.87221 82.78177 start vw surface at 0.1900000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 210738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42299 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94503 mr = 152737 m= 23656 mr = 73722 m= 3366 mr = 16945 m= 187 mr = 1990 m= 2 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.460000 number of dielectric boundary points 86969 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 36139 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) : 1.534990 object centre at (A) : 9.405001 1.689000 30.84150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1376080 0.4569136 midg,1,midg; midg,igrid,midg 0.2799579 -0.2927377 1,midg,midg; igrid,midg,midg -1.5756298E-02 0.1741212 gauss-seidel spectral radius is 0.9991686 estimated iterations to convergence 274 setup time was (sec) 1.760000 now iterating at: 17:16:59 rms-change max change #iterations 10.30004 262.8665 at 10iterations 5.900131 155.6690 at 20iterations 3.361607 73.51047 at 30iterations 1.903380 41.41632 at 40iterations 1.073883 21.23956 at 50iterations 0.6028168 13.92692 at 60iterations 0.3390921 6.711058 at 70iterations 0.1896645 4.702623 at 80iterations 0.1063049 2.186833 at 90iterations 5.9386451E-02 1.274110 at 100iterations 3.3085853E-02 0.6756496 at 110iterations 1.8511036E-02 0.3682060 at 120iterations 1.0354930E-02 0.2086639 at 130iterations 5.7934159E-03 0.1058040 at 140iterations 3.2564502E-03 6.3101768E-02 at 150iterations 1.8424803E-03 3.8633823E-02 at 160iterations 1.0645675E-03 2.3101807E-02 at 170iterations 6.3612504E-04 1.3999939E-02 at 180iterations finished qdiffx linear iterations at : 17:17:09 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 6.3612504E-04 1.3999939E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 17:17:10 12.406u 0.209s 0:12.90 97.6% 0+0k 0+0io 0pf+0w