Sat Oct 15 11:28:05 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+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 Sat Oct 15 2011 at 11:28:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3347 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: 0.5424927 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): -11.47200 41.84300 ymin,ymax (A): -38.50200 27.12100 zmin,zma (A): -15.98900 34.14600 x,y,z range (A): 53.31500 65.62300 50.13500 scale (grids/A): 0.5424927 object centre (A): 15.18550 -5.690501 9.078501 number of atom coordinates read : 3347 total number of charged atoms : 3204 net assigned charge : -0.4999944 assigned positive charge : 498.7806 centred at (gu) : 90.17829 91.69145 90.59743 assigned negative charge : -499.2819 centred at (gu) : 90.16653 91.63959 90.55390 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6437 nv = 96 ne = 84 npr = 67346 no. pairs analyzed = 67346 no. exposed pairs = 4078 no. arc points = 28119 no. surface atoms = 1378 nbur = 1969 mkacc time = 0.1200000 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 = 1.568000 m= 281 mr = 3509 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2960 ## 418 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8496 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7623551E-10 2.8776900E-10 midg,1,midg; midg,igrid,midg -2.4637550E-10 4.6447030E-10 1,midg,midg; igrid,midg,midg -1.0734388E-10 4.3129975E-11 gauss-seidel spectral radius is 0.9825093 estimated iterations to convergence 62 setup time was (sec) 0.4600000 now iterating at: 11:28:05 rms-change max change #iterations 7.4688084E-02 11.29247 at 10iterations 5.0559761E-03 0.7461491 at 20iterations 4.1349774E-04 6.3618660E-02 at 30iterations 6.2101062E-05 9.2773438E-03 at 40iterations 1.4014975E-05 2.3155212E-03 at 50iterations finished qdiffx linear iterations at : 11:28:09 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 1.4014975E-05 2.3155212E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 11:28:09 4.031u 0.212s 0:04.59 92.3% 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 Sat Oct 15 2011 at 11:28:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3347 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: 1.627478 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): -11.47200 41.84300 ymin,ymax (A): -38.50200 27.12100 zmin,zma (A): -15.98900 34.14600 x,y,z range (A): 53.31500 65.62300 50.13500 scale (grids/A): 1.627478 object centre (A): 15.18550 -5.690501 9.078501 number of atom coordinates read : 3347 total number of charged atoms : 3204 net assigned charge : -0.4999944 assigned positive charge : 498.7806 centred at (gu) : 90.53394 95.07351 91.79174 assigned negative charge : -499.2819 centred at (gu) : 90.49943 94.91826 91.66117 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71938 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28119 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23546 mr = 50530 m= 2402 mr = 16645 m= 75 mr = 1158 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 393 time to turn everything in is 0.3700000 number of dielectric boundary points 29624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 402 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 24583 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) : 0.5424927 object centre at (A) : 15.18550 -5.690501 9.078501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6400344E-03 4.2599663E-03 midg,1,midg; midg,igrid,midg 6.6994415E-03 1.4430955E-02 1,midg,midg; igrid,midg,midg 1.7138970E-03 -1.1059174E-03 gauss-seidel spectral radius is 0.9982039 estimated iterations to convergence 187 setup time was (sec) 0.6300000 now iterating at: 11:28:10 rms-change max change #iterations 3.505800 146.1454 at 10iterations 1.467701 54.61841 at 20iterations 0.6159974 21.49330 at 30iterations 0.2585211 8.088970 at 40iterations 0.1083948 3.785151 at 50iterations 4.5594696E-02 1.838180 at 60iterations 1.9150138E-02 0.6871567 at 70iterations 8.0580236E-03 0.2772212 at 80iterations 3.3976964E-03 0.1122775 at 90iterations 1.4376530E-03 4.7836304E-02 at 100iterations 6.1289425E-04 2.2649765E-02 at 110iterations 2.7067796E-04 9.5539093E-03 at 120iterations finished qdiffx linear iterations at : 11:28:19 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 2.7067796E-04 9.5539093E-03 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.410000 DelPhi exited at 11:28:20 9.411u 0.328s 0:10.28 94.6% 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 Sat Oct 15 2011 at 11:28:20 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 = 3347 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.441217 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): -11.47200 41.84300 ymin,ymax (A): -38.50200 27.12100 zmin,zma (A): -15.98900 34.14600 x,y,z range (A): 53.31500 65.62300 50.13500 scale (grids/A): 2.441217 object centre (A): 15.18550 -5.690501 9.078501 number of atom coordinates read : 3347 total number of charged atoms : 3204 net assigned charge : -0.4999944 assigned positive charge : 498.7806 centred at (gu) : 90.80071 97.61001 92.68735 assigned negative charge : -499.2819 centred at (gu) : 90.74925 97.37725 92.49170 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 167100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28119 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 81223 mr = 123062 m= 23807 mr = 65548 m= 3734 mr = 18109 m= 254 mr = 2359 m= 8 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 1493 time to turn everything in is 0.9600000 number of dielectric boundary points 66942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 25605 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) : 1.627478 object centre at (A) : 15.18550 -5.690501 9.078501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1337459 8.0709845E-02 midg,1,midg; midg,igrid,midg 0.1218537 0.4466065 1,midg,midg; igrid,midg,midg 5.2385148E-02 -3.9083958E-03 gauss-seidel spectral radius is 0.9991493 estimated iterations to convergence 271 setup time was (sec) 1.250000 now iterating at: 11:28:21 rms-change max change #iterations 9.049000 314.3834 at 10iterations 5.103864 127.1403 at 20iterations 2.875781 60.48538 at 30iterations 1.607127 34.90935 at 40iterations 0.8961520 18.90591 at 50iterations 0.4983254 10.47502 at 60iterations 0.2774141 5.762722 at 70iterations 0.1539462 3.374008 at 80iterations 8.5121311E-02 1.946939 at 90iterations 4.7111131E-02 0.9976864 at 100iterations 2.6129164E-02 0.5480778 at 110iterations 1.4466454E-02 0.2860031 at 120iterations 8.0075050E-03 0.1569824 at 130iterations 4.4358284E-03 0.1000748 at 140iterations 2.4592883E-03 5.2330017E-02 at 150iterations 1.3680801E-03 2.6658535E-02 at 160iterations 7.6794194E-04 1.4503479E-02 at 170iterations 4.3501431E-04 8.7620020E-03 at 180iterations finished qdiffx linear iterations at : 11:28:37 total time elapsed so far: 16.86000 # loops : 180 mean,max change (kT/e) : 4.3501431E-04 8.7620020E-03 energy calculations done at 16.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.99000 DelPhi exited at 11:28:38 16.995u 0.393s 0:17.81 97.5% 0+0k 0+0io 0pf+0w