Tue Oct 11 06:02:32 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 Tue Oct 11 2011 at 06:02:32 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.7295231 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): 25.62900 73.05800 ymin,ymax (A): -18.80000 29.99900 zmin,zma (A): 3.907000 46.37900 x,y,z range (A): 47.42900 48.79900 42.47200 scale (grids/A): 0.7295231 object centre (A): 49.34350 5.599501 25.14300 number of atom coordinates read : 2290 total number of charged atoms : 1965 net assigned charge : 5.564011 assigned positive charge : 319.4260 centred at (gu) : 88.83778 90.55611 90.28883 assigned negative charge : -313.8622 centred at (gu) : 88.96651 90.49422 90.37581 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7707 nv = 96 ne = 84 npr = 41744 no. pairs analyzed = 41744 no. exposed pairs = 2578 no. arc points = 17685 no. surface atoms = 884 nbur = 1406 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 554 mr = 4503 m= 5 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1582 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8217 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3792656E-07 6.2754637E-09 midg,1,midg; midg,igrid,midg 2.4355533E-08 1.3962581E-07 1,midg,midg; igrid,midg,midg 2.2258740E-07 -2.1468631E-08 gauss-seidel spectral radius is 0.9902029 estimated iterations to convergence 82 setup time was (sec) 0.5000000 now iterating at: 06:02:33 rms-change max change #iterations 0.2274720 29.01268 at 10iterations 3.1409454E-02 3.974007 at 20iterations 4.7171474E-03 0.5876808 at 30iterations 9.9925697E-04 0.1200104 at 40iterations 3.0558827E-04 3.3725739E-02 at 50iterations finished qdiffx linear iterations at : 06:02:35 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 3.0558827E-04 3.3725739E-02 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 06:02:36 3.259u 0.167s 0:03.73 91.4% 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 Tue Oct 11 2011 at 06:02:36 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.188570 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): 25.62900 73.05800 ymin,ymax (A): -18.80000 29.99900 zmin,zma (A): 3.907000 46.37900 x,y,z range (A): 47.42900 48.79900 42.47200 scale (grids/A): 2.188570 object centre (A): 49.34350 5.599501 25.14300 number of atom coordinates read : 2290 total number of charged atoms : 1965 net assigned charge : 5.564011 assigned positive charge : 319.4260 centred at (gu) : 86.51337 91.66841 90.86613 assigned negative charge : -313.8622 centred at (gu) : 86.89939 91.48293 91.12765 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17685 grid for indexing accessible points = 1.400000 m= 34441 mr = 58316 m= 7260 mr = 26440 m= 782 mr = 4999 m= 28 mr = 411 m= 0 mr = 3 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 33587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15630 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) : 0.7295231 object centre at (A) : 49.34350 5.599501 25.14300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2350173E-02 2.5990603E-02 midg,1,midg; midg,igrid,midg 4.4355076E-02 2.9597223E-02 1,midg,midg; igrid,midg,midg 5.3939242E-02 -4.3288447E-02 gauss-seidel spectral radius is 0.9988931 estimated iterations to convergence 238 setup time was (sec) 0.9000000 now iterating at: 06:02:37 rms-change max change #iterations 4.916385 189.3391 at 10iterations 2.473436 85.58810 at 20iterations 1.256624 38.49677 at 30iterations 0.6343512 18.79716 at 40iterations 0.3205967 9.409369 at 50iterations 0.1628107 4.736534 at 60iterations 8.2427859E-02 2.397978 at 70iterations 4.1965403E-02 1.228104 at 80iterations 2.1478098E-02 0.5803273 at 90iterations 1.1170956E-02 0.3338501 at 100iterations 5.8565941E-03 0.1742172 at 110iterations 3.2102878E-03 9.1041565E-02 at 120iterations finished qdiffx linear iterations at : 06:02:43 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 3.2102878E-03 9.1041565E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 06:02:44 7.671u 0.225s 0:08.29 95.1% 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 Tue Oct 11 2011 at 06:02:44 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 3.282854 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): 25.62900 73.05800 ymin,ymax (A): -18.80000 29.99900 zmin,zma (A): 3.907000 46.37900 x,y,z range (A): 47.42900 48.79900 42.47200 scale (grids/A): 3.282854 object centre (A): 49.34350 5.599501 25.14300 number of atom coordinates read : 2290 total number of charged atoms : 1965 net assigned charge : 5.564011 assigned positive charge : 319.4260 centred at (gu) : 84.77003 92.50270 91.29914 assigned negative charge : -313.8622 centred at (gu) : 85.34907 92.22438 91.69147 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 187048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17685 grid for indexing accessible points = 1.400000 m= 105104 mr = 139666 m= 45095 mr = 88142 m= 13866 mr = 37628 m= 3056 mr = 10989 m= 417 mr = 2203 m= 12 mr = 275 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.910000 number of dielectric boundary points 75695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 15720 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) : 2.188570 object centre at (A) : 49.34350 5.599501 25.14300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5418602E-02 0.2114685 midg,1,midg; midg,igrid,midg 0.3273707 0.1659459 1,midg,midg; igrid,midg,midg 0.5065851 -0.4970533 gauss-seidel spectral radius is 0.9993151 estimated iterations to convergence 301 setup time was (sec) 2.220000 now iterating at: 06:02:47 rms-change max change #iterations 10.76966 360.5594 at 10iterations 6.442331 128.2510 at 20iterations 3.835855 74.26167 at 30iterations 2.291284 42.42496 at 40iterations 1.360741 27.36961 at 50iterations 0.8058338 15.03714 at 60iterations 0.4773347 7.914875 at 70iterations 0.2826403 4.705299 at 80iterations 0.1672480 2.906487 at 90iterations 9.9053867E-02 1.805573 at 100iterations 5.8628712E-02 0.9768524 at 110iterations 3.5128504E-02 0.5721376 at 120iterations 2.1225469E-02 0.4484444 at 130iterations 1.3113549E-02 0.2756042 at 140iterations 8.4110349E-03 0.1487579 at 150iterations 5.6674052E-03 0.1008987 at 160iterations 4.0553394E-03 7.0659637E-02 at 170iterations 3.0781049E-03 5.2307129E-02 at 180iterations finished qdiffx linear iterations at : 06:02:57 total time elapsed so far: 12.49000 # loops : 180 mean,max change (kT/e) : 3.0781049E-03 5.2307129E-02 energy calculations done at 12.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 06:02:57 12.665u 0.211s 0:13.14 97.9% 0+0k 0+0io 0pf+0w